X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD-M%2Freadrtns_CSA.F;h=d0c10c759cdb4757057eaf1e8a9e876f23bf94e6;hb=d7cc63e0eaffacfa27154f01a5a14d0b6d14d7ea;hp=79840a4579fa4e63dd95ecc5e767a1d143bed3ff;hpb=aedd2f72960d9cec69fcc7f0b6fd6555c7e22312;p=unres.git

diff --git a/source/unres/src_MD-M/readrtns_CSA.F b/source/unres/src_MD-M/readrtns_CSA.F
index 79840a4..d0c10c7 100644
--- a/source/unres/src_MD-M/readrtns_CSA.F
+++ b/source/unres/src_MD-M/readrtns_CSA.F
@@ -104,7 +104,7 @@ C constrains on theta angles WITH_THETA_CONSTR is the keyword
       with_theta_constr = index(controlcard,"WITH_THETA_CONSTR").gt.0
       write (iout,*) "with_theta_constr ",with_theta_constr
       call readi(controlcard,'SYM',symetr,1)
-      call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
+      call reada(controlcard,'TIMLIM',timlim,2800.0D0) ! default 16 hours
       unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
       call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
       call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
@@ -145,6 +145,8 @@ C constrains on theta angles WITH_THETA_CONSTR is the keyword
       AFMlog=(index(controlcard,'AFM'))
       selfguide=(index(controlcard,'SELFGUIDE'))
       print *,'AFMlog',AFMlog,selfguide,"KUPA"
+      call readi(controlcard,'TUBEMOD',tubelog,0)
+      write (iout,*) TUBElog,"TUBEMODE"
       call readi(controlcard,'IPRINT',iprint,0)
 C SHIELD keyword sets if the shielding effect of side-chains is used
 C 0 denots no shielding is used all peptide are equally despite the 
@@ -179,6 +181,7 @@ C      if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
         else
           icheckgrad=3
         endif
+        call reada(controlcard,'DELTA',aincr,1.0d-7)
       elseif (index(controlcard,'THREAD').gt.0) then
         modecalc=2
         call readi(controlcard,'THREAD',nthread,0)
@@ -262,6 +265,16 @@ C      endif
       write(iout,*) "bufliptop=",bufliptop
       write(iout,*) "buflipbot=",buflipbot
       write (iout,*) "SHIELD MODE",shield_mode
+      if (TUBElog.gt.0) then
+       call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
+       call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
+       call reada(controlcard,"RTUBE",tubeR0,0.0d0)
+       call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
+       call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
+       call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
+       buftubebot=bordtubebot+tubebufthick
+       buftubetop=bordtubetop-tubebufthick
+      endif
       if (shield_mode.gt.0) then
       pi=3.141592d0
 C VSolvSphere the volume of solving sphere
@@ -600,6 +613,7 @@ C
       include 'COMMON.BOUNDS'
       include 'COMMON.MD'
       include 'COMMON.SETUP'
+      include 'COMMON.SHIELD'
       character*4 sequence(maxres)
       integer rescode
       double precision x(maxvar)
@@ -641,7 +655,9 @@ C Read weights of the subsequent energy terms.
        call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
        call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
        call reada(weightcard,'TEMP0',temp0,300.0d0)
+       call reada(weightcard,'WSHIELD',wshield,1.0d0)
        call reada(weightcard,'WLT',wliptran,0.0D0)
+       call reada(weightcard,'WTUBE',wtube,1.0D0)
        if (index(weightcard,'SOFT').gt.0) ipot=6
 C 12/1/95 Added weight for the multi-body term WCORR
        call reada(weightcard,'WCORRH',wcorr,1.0D0)
@@ -750,10 +766,16 @@ C 12/1/95 Added weight for the multi-body term WCORR
       call reada(weightcard,"BTRISS",btriss,0.021D0)
       call reada(weightcard,"CTRISS",ctriss,1.001D0)
       call reada(weightcard,"DTRISS",dtriss,1.001D0)
+      call reada(weightcard,"LIPSCALE",lipscale,1.3D0)
       write (iout,*) "ATRISS=", atriss
       write (iout,*) "BTRISS=", btriss
       write (iout,*) "CTRISS=", ctriss
       write (iout,*) "DTRISS=", dtriss
+       if (shield_mode.gt.0) then
+        lipscale=0.0d0
+        write (iout,*) "liscale not used in shield mode"
+       endif
+      write (iout,*) "lipid scaling factor", lipscale
       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
       do i=1,maxres
         dyn_ss_mask(i)=.false.
@@ -780,7 +802,7 @@ C 12/1/95 Added weight for the multi-body term WCORR
           ss_depth=0.0
         endif
       endif
-
+      write (iout,*) "wshield,", wshield
       if(me.eq.king.or..not.out1file) then
        write (iout,*) "Parameters of the SS-bond potential:"
        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
@@ -1038,7 +1060,7 @@ c----------------------
           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
           stop 'Error reading reference structure'
 #endif
-   39     call chainbuild
+   39     call chainbuild_extconf
           call setup_var
 czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
           nstart_sup=nnt
@@ -1111,6 +1133,7 @@ C initial geometry.
             return
           else
             call read_angles(inp,*36)
+            call chainbuild_extconf
           endif
           goto 37
    36     write (iout,'(a)') 'Error reading angle file.'
@@ -2127,6 +2150,8 @@ C Get parameter filenames and open the parameter files.
       open (irotam_pdb,file=rotname_pdb,status='old',action='read')
 #endif
 #endif
+      call getenv_loc('TUBEPAR',tubename)
+      open (itube,file=tubename,status='old',readonly)
 #ifndef OLDSCP
 C
 C 8/9/01 In the newest version SCp interaction constants are read from a file