1)Clean-up 2)making similar src_MD and its multichain version 3)

correction of potentials and bugfix in ../PARAM/pot_theta_G631_DIL.parm
4) introduction of theta_pdb and rotam_pdb in multichain

diff --git a/PARAM/pot_theta_G631_DIL.parm b/PARAM/pot_theta_G631_DIL.parm
index 3b94e8b..494bff1 100644 (file)
--- a/PARAM/pot_theta_G631_DIL.parm
+++ b/PARAM/pot_theta_G631_DIL.parm
@@ -1,5 +1,5 @@
 2 10 4 4 6 4
-1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 2
+1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 2 3
 Gppreg
     4.58415E+01 
     1.05721E+03 

diff --git a/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k b/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
index d66c9c9..f371faa 100644 (file)
--- a/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+++ b/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
@@ -4,71 +4,101 @@
    5.263842382200000   5.496195412400000   4.292812416200000   4.358225054000000
    4.266775592100000   3.681384595800000   3.540542964700000   3.702698591200000
    4.717759615600000   3.381199222700000   3.793608545800000   4.515749058500000
+
    6.629674668000000   6.671726050800000   6.816887694500000   6.837896015200000
    6.351203998600000   6.142519242300000   5.520020640600000   5.485893602400000
    4.938257326200000   4.279512916600000   4.053485701800000   4.208642852500000
    3.538808627900000   3.420973032700000   2.799574419300000   4.816426855300000
-   3.879075507100000   3.587826217700000   4.645743255500000   5.434261193691611
-   6.009504353949445   5.751833613689151   4.388369927131041   6.139482146000000
-   4.432779364180328   3.635448013213493   3.042556269070575   1.858255457238648
-   3.619846653665197   3.902273188000000   2.840826371233924   1.901219059651194
-   3.010635482615414   2.681361243261458   3.871192813400000   3.639660062795308
-   4.487266103000000   7.144249845164532   5.950132764851209   5.636408114630104
-   6.256568766200000   4.721753486138623   5.072743940945156   4.725634408062251
-   3.773513014441411   3.537762800513723   4.309235277900000   4.002278495651890
-   4.124103654261368   1.771213000543424   3.864752062532702   4.468184401000000
-   4.481956278333824   4.902394508200000   5.956274037802311   7.211686591187319
-   6.204787608200000   5.376059458542183   5.023511032618925   3.156887023825594
-   2.932344993803476   2.999897908513799   3.895407345300000   2.991138620007669
-   2.096199593475473   1.780803572610500   3.558049006448599   4.023841260600000
-   3.682633555857166   4.808718037700000   5.741243604492526   5.884448203300000
-   3.398137040446693   5.432746439707773   4.729707784043235   3.970010356404483
-   3.414577863946629   3.650628980600000   2.605234605568324   2.392978757746573
-   3.096075853472831   4.009206356643173   3.441595274000000   3.721594130855455
-   4.593424600900000   5.282881132500000   4.829846631500000   4.757532777700000
-   4.724977904200000   3.565638428500000   3.561336656700000   3.927304556400000
-   3.766477911800000   3.586169976100000   3.552319162700000   4.650867246300000
-   4.242430826000000   4.098772778300000   4.507966992900000   4.222264575400000
-   3.568880377430671   1.710507474941357   0.726915001472055   2.519422404183540
-   3.136598518800000   2.564808696931206   3.101026335222954   2.213396947938416
-   3.343125814753411   3.444306825200000   2.416478592751639   4.091530576300000
+   3.879075507100000   3.587826217700000   4.645743255500000
+
+   5.434261193691611   6.009504353949445   5.751833613689151   4.388369927131041
+   6.139482146000000   4.432779364180328   3.635448013213493   3.042556269070575
+   1.858255457238648   3.619846653665197   3.902273188000000   2.840826371233924
+   1.901219059651194   3.010635482615414   2.681361243261458   3.871192813400000
+   3.639660062795308   4.487266103000000
+
+   7.144249845164532   5.950132764851209   5.636408114630104   6.256568766200000
+   4.721753486138623   5.072743940945156   4.725634408062251   3.773513014441411
+   3.537762800513723   4.309235277900000   4.002278495651890   4.124103654261368
+   1.771213000543424   3.864752062532702   4.468184401000000   4.481956278333824
+   4.902394508200000
+
+   5.956274037802311   7.211686591187319   6.204787608200000   5.376059458542183
+   5.023511032618925   3.156887023825594   2.932344993803476   2.999897908513799
+   3.895407345300000   2.991138620007669   2.096199593475473   1.780803572610500
+   3.558049006448599   4.023841260600000   3.682633555857166   4.808718037700000
+
+   5.741243604492526   5.884448203300000   3.398137040446693   5.432746439707773
+   4.729707784043235   3.970010356404483   3.414577863946629   3.650628980600000
+   2.605234605568324   2.392978757746573   3.096075853472831   4.009206356643173
+   3.441595274000000   3.721594130855455   4.593424600900000
+
+   5.282881132500000   4.829846631500000   4.757532777700000   4.724977904200000
+   3.565638428500000   3.561336656700000   3.927304556400000   3.766477911800000
+   3.586169976100000   3.552319162700000   4.650867246300000   4.242430826000000
+   4.098772778300000   4.507966992900000
+
+   4.222264575400000   3.568880377430671   1.710507474941357   0.726915001472055
+   2.519422404183540   3.136598518800000   2.564808696931206   3.101026335222954
+   2.213396947938416   3.343125814753411   3.444306825200000   2.416478592751639
+   4.091530576300000
+
    4.157487725645439   3.262380685905436   2.953659747759453   1.237209789211462
    2.500185737000000   1.984183152198450   1.368828812773212   2.060401072298498
    2.863410468895249   2.015232903800000   1.541966676954322   3.639585254600000
+
    2.501655793500000   2.394681323067151   2.071384505085577   1.074154474700000
    0.985099710786774   0.001985439127056   0.921773098679111   5.126752085199419
-   1.500212764900000  -0.018286801754111   3.538112898500000   2.248058879145623
-   2.683627337507786   1.505360785600000  -0.706299059260768   1.284606704482992
-   1.109202790492530   2.070407759035996   1.983305353800000  -0.008577364700000
-   2.955755366600000   1.280003824300000   0.768980610000000   0.625889188870640
-   1.535343520692143   0.574105444778441   1.174671233709513   1.497548217400000
-  -0.665902088339257   2.941502147900000  -0.679242885900000   0.453238323900000
-  -0.759038766000000  -0.361703484600000   1.680327505800000   0.677520998800000
-  -0.535483746800000   2.620859136300000   0.290068410287431  -0.092399325129687
-   1.982203632452388   0.078357579868221   0.389638827500000  -0.177470106993247
-   2.325532607700000  -3.392465857895507  -1.871634582322480   1.071505323254014
-   2.748917412400000   1.802089391960750   1.797571866700000  -1.397996047062832
-   0.263585152937208   2.820287379000000   1.642062410367716   1.862509124700000
+   1.500212764900000  -0.018286801754111   3.538112898500000
+
+   2.248058879145623   2.683627337507786   1.505360785600000  -0.706299059260768
+   1.284606704482992   1.109202790492530   2.070407759035996   1.983305353800000
+  -0.008577364700000   2.955755366600000
+
+   1.280003824300000   0.768980610000000   0.625889188870640   1.535343520692143
+   0.574105444778441   1.174671233709513   1.497548217400000  -0.665902088339257
+   2.941502147900000
+
+  -0.679242885900000   0.453238323900000  -0.759038766000000  -0.361703484600000
+   1.680327505800000   0.677520998800000  -0.535483746800000   2.620859136300000 
+
+   0.290068410287431  -0.092399325129687   1.982203632452388   0.078357579868221
+   0.389638827500000  -0.177470106993247   2.325532607700000
+
+  -3.392465857895507  -1.871634582322480   1.071505323254014   2.748917412400000
+   1.802089391960750   1.797571866700000
+
+  -1.397996047062832   0.263585152937208   2.820287379000000   1.642062410367716
+   1.862509124700000
+
    3.729277869700000   2.294443648100000  -0.070327972331951   3.111577617700000
-  -0.082736296100000  -1.604311318200000   2.443983743500000  -3.048709356063184
-   2.366463453300000   4.192796926000000   2.674806001700000   2.733881014500000
-   2.966464722900000   2.881963673700000   3.021073815000000   2.841428615200000
-   2.477343866000000   2.461194378800000   2.465320121300000   2.492508737100000
-   2.573476775100000   2.456402674400000   2.484782528100000   2.488928923300000
-   2.508951764500000   2.508333838300000   2.422062272300000   2.271460977000000
-   2.452070308900000   2.702612978800000   4.927215476100000   5.105428423000000
-   4.207351616500000   4.851397283700000   2.784887529300000   3.582986163400000
-   7.866021757600000   7.429920984700000   1.962593983200000   0.798776956900000
-   4.058089968100000   1.888902103200000   3.198719702600000   3.267327453800000
-   2.684813190400000   2.004302740400000   6.244634191000000   8.195945209500000
-  13.474829585800000   2.663237683700000   0.869902301100000   1.054066001400000
-   0.938590929800000   1.026327410100000   1.083527704500000   1.054318388600000
-   0.788868699600000   0.898930583300000   1.003996287500000   1.242751812800000
-   0.893280172400000   0.917392899000000   1.615769565700000   1.431586037300000
-   2.049831787900000   1.419961554600000   0.993367797100000   1.431962560000000
-  27.495176328800000   0.778802528600000   0.010369755600000   0.061138567400000
-   0.044830334600000   0.039283178200000   0.085416633800000   0.039889661900000
-   0.024949656900000   0.023241090800000   0.086137910000000  -0.075479418500000
-  -0.026614602100000  -0.016342909900000   0.057216710300000  -0.046860882500000
-   0.015104845500000   0.008496367800000   0.027893039700000   0.007692291100000
-   0.103353673800000  -0.009825603600000
+
+  -0.082736296100000  -1.604311318200000   2.443983743500000
+
+  -3.048709356063184   2.366463453300000
+
+   4.192796926000000
+
+   2.674806001700000   2.733881014500000   2.966464722900000   2.881963673700000
+   3.021073815000000   2.841428615200000   2.477343866000000   2.461194378800000
+   2.465320121300000   2.492508737100000   2.573476775100000   2.456402674400000
+   2.484782528100000   2.488928923300000   2.508951764500000   2.508333838300000
+   2.422062272300000   2.271460977000000   2.452070308900000   2.702612978800000
+
+   4.927215476100000   5.105428423000000   4.207351616500000   4.851397283700000
+   2.784887529300000   3.582986163400000   7.866021757600000   7.429920984700000
+   1.962593983200000   0.798776956900000   4.058089968100000   1.888902103200000
+   3.198719702600000   3.267327453800000   2.684813190400000   2.004302740400000
+   6.244634191000000   8.195945209500000  13.474829585800000   2.663237683700000
+
+   0.869902301100000   1.054066001400000   0.938590929800000   1.026327410100000
+   1.083527704500000   1.054318388600000   0.788868699600000   0.898930583300000
+   1.003996287500000   1.242751812800000   0.893280172400000   0.917392899000000
+   1.615769565700000   1.431586037300000   2.049831787900000   1.419961554600000
+   0.993367797100000   1.431962560000000  27.495176328800000   0.778802528600000
+
+   0.010369755600000   0.061138567400000   0.044830334600000   0.039283178200000
+   0.085416633800000   0.039889661900000   0.024949656900000   0.023241090800000
+   0.086137910000000  -0.075479418500000  -0.026614602100000  -0.016342909900000
+   0.057216710300000  -0.046860882500000   0.015104845500000   0.008496367800000
+   0.027893039700000   0.007692291100000   0.103353673800000  -0.009825603600000

diff --git a/source/unres/src_MD-M/COMMON.IOUNITS b/source/unres/src_MD-M/COMMON.IOUNITS
index a9ace0b..49b6db3 100644 (file)
--- a/source/unres/src_MD-M/COMMON.IOUNITS
+++ b/source/unres/src_MD-M/COMMON.IOUNITS
@@ -11,11 +11,11 @@ C General I/O units & files
       integer inp,iout,igeom,intin,ipdb,imol2,ipdbin,ithep,irotam,
      &        itorp,itordp,ifourier,ielep,isidep,iscpp,icbase,istat,
      &        ientin,ientout,izs1,isecpred,ibond,irest2,iifrag,icart,
-     &        irest1,isccor
+     &        irest1,isccor,ithep_pdb,irotam_pdb
       common /iounits/ inp,iout,igeom,intin,ipdb,imol2,ipdbin,ithep,
      &        irotam,itorp,itordp,ifourier,ielep,isidep,iscpp,icbase,
      &        istat,ientin,ientout,izs1,isecpred,ibond,irest2,iifrag,
-     &        icart,irest1,isccor
+     &        icart,irest1,isccor,ithep_pdb,irotam_pdb
       character*256 outname,intname,pdbname,mol2name,statname,intinname,
      &        entname,prefix,secpred,rest2name,qname,cartname,tmpdir,
      &        mremd_rst_name,curdir,pref_orig
@@ -38,9 +38,11 @@ C CSA I/O units & files
      & icsa_bank_reminimized,icsa_native_int,icsa_in,icsa_pdb
 C Parameter files
       character*256 bondname,thetname,rotname,torname,tordname,
-     &       fouriername,elename,sidename,scpname,sccorname,patname
+     &       fouriername,elename,sidename,scpname,sccorname,patname,
+     &       thetname_pdb,rotname_pdb
       common /parfiles/ bondname,thetname,rotname,torname,tordname,
-     &       fouriername,elename,sidename,scpname,sccorname,patname
+     &       fouriername,elename,sidename,scpname,sccorname,patname,
+     &       thetname_pdb,rotname_pdb
       character*3 pot
 C-----------------------------------------------------------------------
 C INP    - main input file

diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F
index b651f0a..b7e216c 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -5116,7 +5116,7 @@ c        write (2,*) "xx",xx," yy",yy," zz",zz
 Cc diagnostics - remove later
         xx1 = dcos(alph(2))
         yy1 = dsin(alph(2))*dcos(omeg(2))
-        zz1 = -dsign(1.0,itype(i))*dsin(alph(2))*dsin(omeg(2))
+        zz1 = -dsign(1.0,dfloat(itype(i)))*dsin(alph(2))*dsin(omeg(2))
         write(2,'(3f8.1,3f9.3,1x,3f9.3)') 
      &    alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
      &    xx1,yy1,zz1

diff --git a/source/unres/src_MD-M/initialize_p.F b/source/unres/src_MD-M/initialize_p.F
index a91149e..ed6b83c 100644 (file)
--- a/source/unres/src_MD-M/initialize_p.F
+++ b/source/unres/src_MD-M/initialize_p.F
@@ -80,7 +80,9 @@ C
       igeom=  8
       intin=  9
       ithep= 11
+      ithep_pdb=51
       irotam=12
+      irotam_pdb=52
       itorp= 13
       itordp= 23
       ielep= 14

diff --git a/source/unres/src_MD-M/parmread.F b/source/unres/src_MD-M/parmread.F
index 154fcf4..6ea0840 100644 (file)
--- a/source/unres/src_MD-M/parmread.F
+++ b/source/unres/src_MD-M/parmread.F
@@ -388,13 +388,15 @@ C
       enddo
       call flush(iout)
       endif
-      write (2,*) "Start reading THETA_PDB"
+      write (2,*) "Start reading THETA_PDB",ithep_pdb
       do i=1,ntyp
-        read (ithep,*,err=111,end=111) a0thet(i),(athet(j,i,1,1),j=1,2),
+c      write (2,*) 'i=',i
+        read (ithep_pdb,*,err=111,end=111)
+     &     a0thet(i),(athet(j,i,1,1),j=1,2),
      &    (bthet(j,i,1,1),j=1,2)
-        read (ithep,*,err=111,end=111) (polthet(j,i),j=0,3)
-        read (ithep,*,err=111,end=111) (gthet(j,i),j=1,3)
-        read (ithep,*,err=111,end=111) theta0(i),sig0(i),sigc0(i)
+        read (ithep_pdb,*,err=111,end=111) (polthet(j,i),j=0,3)
+        read (ithep_pdb,*,err=111,end=111) (gthet(j,i),j=1,3)
+        read (ithep_pdb,*,err=111,end=111) theta0(i),sig0(i),sigc0(i)
         sigc0(i)=sigc0(i)**2
       enddo
       do i=1,ntyp
@@ -539,6 +541,7 @@ C
 C Read the parameters of the probability distribution/energy expression
 C of the side chains.
 C
+      write (2,*) "Start reading ROTAM_PDB"
       do i=1,ntyp
         read (irotam_pdb,'(3x,i3,f8.3)',end=112,err=112) nlob(i),dsc(i)
         if (i.eq.10) then
@@ -577,6 +580,7 @@ C
         endif
       enddo
       close (irotam_pdb)
+      write (2,*) "End reading ROTAM_PDB"
 #endif
       close(irotam)
 

diff --git a/source/unres/src_MD-M/readrtns_CSA.F b/source/unres/src_MD-M/readrtns_CSA.F
index 7ac0669..265b705 100644 (file)
--- a/source/unres/src_MD-M/readrtns_CSA.F
+++ b/source/unres/src_MD-M/readrtns_CSA.F
@@ -1916,12 +1916,22 @@ C Get parameter filenames and open the parameter files.
       open (itordp,file=tordname,status='old',readonly)
       call getenv_loc('SCCORPAR',sccorname)
       open (isccor,file=sccorname,status='old',readonly)
+#ifndef CRYST_THETA
+      call getenv_loc('THETPARPDB',thetname_pdb)
+      print *,"thetname_pdb ",thetname_pdb
+      open (ithep_pdb,file=thetname_pdb,status='old',action='read')
+      print *,ithep_pdb," opened"
+#endif
       call getenv_loc('FOURIER',fouriername)
       open (ifourier,file=fouriername,status='old',readonly)
       call getenv_loc('ELEPAR',elename)
       open (ielep,file=elename,status='old',readonly)
       call getenv_loc('SIDEPAR',sidename)
       open (isidep,file=sidename,status='old',readonly)
+#ifndef CRYST_SC
+      call getenv_loc('ROTPARPDB',rotname_pdb)
+      open (irotam_pdb,file=rotname_pdb,status='old',action='read')
+#endif
 #endif
 #ifndef OLDSCP
 C
@@ -2083,6 +2093,8 @@ C Write file names
      &  thetname(:ilen(thetname))
       write (iout,*) "Rotamer parameter file          : ",
      &  rotname(:ilen(rotname))
+      write (iout,*) "Thetpdb parameter file          : ",
+     &  thetname_pdb(:ilen(thetname_pdb))
       write (iout,*) "Threading database              : ",
      &  patname(:ilen(patname))
       if (lentmp.ne.0) 

diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F
index ba31354..bb85d93 100644 (file)
--- a/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@ -4791,7 +4791,7 @@ C
         dephii=0.0d0
         dephii1=0.0d0
         theti2=0.5d0*theta(i)
-        ityp2=ithetyp(iabs(itype(i-1)))
+        ityp2=ithetyp(itype(i-1))
         do k=1,nntheterm
           coskt(k)=dcos(k*theti2)
           sinkt(k)=dsin(k*theti2)
@@ -4803,7 +4803,7 @@ C
 #else
           phii=phi(i)
 #endif
-          ityp1=ithetyp(iabs(itype(i-2)))
+          ityp1=ithetyp(itype(i-2))
           do k=1,nsingle
             cosph1(k)=dcos(k*phii)
             sinph1(k)=dsin(k*phii)
@@ -4817,6 +4817,9 @@ C
           enddo 
         endif
         if (i.lt.nres) then
+
+        if (iabs(itype(i+1)).eq.20) iblock=2
+        if (iabs(itype(i+1)).ne.20) iblock=1
 #ifdef OSF
           phii1=phi(i+1)
           if (phii1.ne.phii1) phii1=150.0
@@ -4824,7 +4827,7 @@ C
 #else
           phii1=phi(i+1)
 #endif
-          ityp3=ithetyp(iabs(itype(i)))
+          ityp3=ithetyp(itype(i))
           do k=1,nsingle
             cosph2(k)=dcos(k*phii1)
             sinph2(k)=dsin(k*phii1)
@@ -4837,7 +4840,7 @@ C
             sinph2(k)=0.0d0
           enddo
         endif  
-        ethetai=aa0thet(ityp1,ityp2,ityp3)
+         ethetai=aa0thet(ityp1,ityp2,ityp3,iblock)
         do k=1,ndouble
           do l=1,k-1
             ccl=cosph1(l)*cosph2(k-l)
@@ -4859,11 +4862,12 @@ C
         enddo
         endif
         do k=1,ntheterm
-          ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
-          dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
+          ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3,iblock)*sinkt(k)
+          dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3,iblock)
      &      *coskt(k)
           if (lprn)
-     &    write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
+     &    write (iout,*) "k",k,
+     &    "aathet",aathet(k,ityp1,ityp2,ityp3,iblock),
      &     " ethetai",ethetai
         enddo
         if (lprn) then
@@ -4882,24 +4886,24 @@ C
         endif
         do m=1,ntheterm2
           do k=1,nsingle
-            aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
-     &         +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
-     &         +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
-     &         +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
+            aux=bbthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)
+     &         +ccthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k)
+     &         +ddthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)
+     &         +eethet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k)
             ethetai=ethetai+sinkt(m)*aux
             dethetai=dethetai+0.5d0*m*aux*coskt(m)
             dephii=dephii+k*sinkt(m)*(
-     &          ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
-     &          bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
+     &          ccthet(k,m,ityp1,ityp2,ityp3,iblock)*cosph1(k)-
+     &          bbthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph1(k))
             dephii1=dephii1+k*sinkt(m)*(
-     &          eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
-     &          ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
+     &          eethet(k,m,ityp1,ityp2,ityp3,iblock)*cosph2(k)-
+     &          ddthet(k,m,ityp1,ityp2,ityp3,iblock)*sinph2(k))
             if (lprn)
      &      write (iout,*) "m",m," k",k," bbthet",
-     &         bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
-     &         ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
-     &         ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
-     &         eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+     &         bbthet(k,m,ityp1,ityp2,ityp3,iblock)," ccthet",
+     &         ccthet(k,m,ityp1,ityp2,ityp3,iblock)," ddthet",
+     &         ddthet(k,m,ityp1,ityp2,ityp3,iblock)," eethet",
+     &         eethet(k,m,ityp1,ityp2,ityp3,iblock)," ethetai",ethetai
           enddo
         enddo
         if (lprn)
@@ -4907,28 +4911,33 @@ C
         do m=1,ntheterm3
           do k=2,ndouble
             do l=1,k-1
-              aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
-     &            ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
-     &            ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
-     &            ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
+       aux=ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+     & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l)+
+     & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+     & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)
+
               ethetai=ethetai+sinkt(m)*aux
               dethetai=dethetai+0.5d0*m*coskt(m)*aux
               dephii=dephii+l*sinkt(m)*(
-     &           -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
-     &            ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
-     &            ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
-     &            ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+     & -ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)-
+     &  ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+     &  ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)+
+     &  ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
+
               dephii1=dephii1+(k-l)*sinkt(m)*(
-     &           -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
-     &            ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
-     &            ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
-     &            ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
+     &-ffthet(l,k,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(l,k)+
+     & ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)*sinph1ph2(k,l)+
+     & ggthet(l,k,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(l,k)-
+     & ggthet(k,l,m,ityp1,ityp2,ityp3,iblock)*cosph1ph2(k,l))
+
               if (lprn) then
               write (iout,*) "m",m," k",k," l",l," ffthet",
-     &            ffthet(l,k,m,ityp1,ityp2,ityp3),
-     &            ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
-     &            ggthet(l,k,m,ityp1,ityp2,ityp3),
-     &            ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
+     &            ffthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+     &            ffthet(k,l,m,ityp1,ityp2,ityp3,iblock)," ggthet",
+     &            ggthet(l,k,m,ityp1,ityp2,ityp3,iblock),
+     &            ggthet(k,l,m,ityp1,ityp2,ityp3,iblock),
+     &            " ethetai",ethetai
+
               write (iout,*) cosph1ph2(l,k)*sinkt(m),
      &            cosph1ph2(k,l)*sinkt(m),
      &            sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
@@ -5280,7 +5289,7 @@ C
         cosfac=dsqrt(cosfac2)
         sinfac2=0.5d0/(1.0d0-costtab(i+1))
         sinfac=dsqrt(sinfac2)
-        it=itype(i)
+        it=iabs(itype(i))
         if (it.eq.10) goto 1
 c
 C  Compute the axes of tghe local cartesian coordinates system; store in
@@ -5298,7 +5307,7 @@ C     &   dc_norm(3,i+nres)
           y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
         enddo
         do j = 1,3
-          z_prime(j) = -uz(j,i-1)
+          z_prime(j) = -uz(j,i-1)*dsign(1.0d0,dfloat(itype(i)))
         enddo     
 c       write (2,*) "i",i
 c       write (2,*) "x_prime",(x_prime(j),j=1,3)
@@ -5320,8 +5329,7 @@ c
         do j = 1,3
           xx = xx + x_prime(j)*dc_norm(j,i+nres)
           yy = yy + y_prime(j)*dc_norm(j,i+nres)
-          zz = zz + dsign(1.0,dfloat(itype(i)))
-     &             *z_prime(j)*dc_norm(j,i+nres)
+          zz = zz + z_prime(j)*dc_norm(j,i+nres)
         enddo
 
         xxtab(i)=xx
@@ -5509,8 +5517,10 @@ c     &   (dC_norm(j,i-1),j=1,3)," vbld_inv",vbld_inv(i+1),vbld_inv(i)
          dZZ_Ci1(k)=0.0d0
          dZZ_Ci(k)=0.0d0
          do j=1,3
-           dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
-           dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
+           dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)
+     &     *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
+           dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)
+     &     *dsign(1.0d0,dfloat(itype(i)))*dC_norm(j,i+nres)
          enddo
           
          dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
@@ -5796,6 +5806,8 @@ c     lprn=.true.
       etors=0.0D0
       do i=iphi_start,iphi_end
       etors_ii=0.0D0
+c        if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+c     &      .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
         itori=itortyp(itype(i-2))
         itori1=itortyp(itype(i-1))
         if (iabs(itype(i)).eq.20) then
@@ -5895,6 +5907,8 @@ C Set lprn=.true. for debugging
 c     lprn=.true.
       etors_d=0.0D0
       do i=iphid_start,iphid_end
+c        if (itype(i-2).eq.ntyp1 .or. itype(i-1).eq.ntyp1
+c     &      .or. itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
         itori=itortyp(itype(i-2))
         itori1=itortyp(itype(i-1))
         itori2=itortyp(itype(i))
@@ -5969,7 +5983,7 @@ c        amino-acid residues.
 C Set lprn=.true. for debugging
       lprn=.false.
 c      lprn=.true.
-c      write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
+c     write (iout,*) "EBACK_SC_COR",itau_start,itau_end
       esccor=0.0D0
       do i=itau_start,itau_end
         esccor_ii=0.0D0
@@ -5995,9 +6009,11 @@ c   3 = SC...Ca...Ca...SCi
      &      (itype(i-1).eq.10).or.(itype(i-2).eq.ntyp1).or.
      &      (itype(i-1).eq.ntyp1)))
      &    .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
-     &     .or.(itype(i-2).eq.ntyp1)))
+     &     .or.(itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)
+     &     .or.(itype(i).eq.ntyp1)))
      &    .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
-     &      (itype(i-1).eq.ntyp1)))) cycle  
+     &      (itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
+     &      (itype(i-3).eq.ntyp1)))) cycle
         if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.ntyp1)) cycle
         if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.ntyp1))
      & cycle
@@ -6014,9 +6030,9 @@ c        write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi
 c     &gloc_sc(intertyp,i-3,icg)
         if (lprn)
      &  write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
-     &  restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
-     &  (v1sccor(j,intertyp,itori,itori1),j=1,6)
-     & ,(v2sccor(j,intertyp,itori,itori1),j=1,6)
+     &  restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,isccori,isccori1,
+     &  (v1sccor(j,intertyp,isccori,isccori1),j=1,6)
+     & ,(v2sccor(j,intertyp,isccori,isccori1),j=1,6)
         gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
        enddo !intertyp
       enddo

diff --git a/source/unres/src_MD/parmread.F b/source/unres/src_MD/parmread.F
index 68f599a..074db7c 100644 (file)
--- a/source/unres/src_MD/parmread.F
+++ b/source/unres/src_MD/parmread.F
@@ -391,11 +391,12 @@ C
       endif
       write (2,*) "Start reading THETA_PDB"
       do i=1,ntyp
-        read (ithep,*,err=111,end=111) a0thet(i),(athet(j,i,1,1),j=1,2),
+        read (ithep_pdb,*,err=111,end=111)
+     &     a0thet(i),(athet(j,i,1,1),j=1,2),
      &    (bthet(j,i,1,1),j=1,2)
-        read (ithep,*,err=111,end=111) (polthet(j,i),j=0,3)
-       read (ithep,*,err=111,end=111) (gthet(j,i),j=1,3)
-       read (ithep,*,err=111,end=111) theta0(i),sig0(i),sigc0(i)
+        read (ithep_pdb,*,err=111,end=111) (polthet(j,i),j=0,3)
+       read (ithep_pdb,*,err=111,end=111) (gthet(j,i),j=1,3)
+       read (ithep_pdb,*,err=111,end=111) theta0(i),sig0(i),sigc0(i)
        sigc0(i)=sigc0(i)**2
       enddo
       do i=1,ntyp
@@ -541,6 +542,8 @@ C
 C Read the parameters of the probability distribution/energy expression
 C of the side chains.
 C
+      write (2,*) "Start reading ROTAM_PDB"
+
       do i=1,ntyp
        read (irotam_pdb,'(3x,i3,f8.3)',end=112,err=112) nlob(i),dsc(i)
         if (i.eq.10) then
@@ -579,6 +582,7 @@ C
        endif
       enddo
       close (irotam_pdb)
+      write (2,*) "Ending reading ROTAM_PDB"
 #endif
       close(irotam)