From b327a9d10f4a8f089bedddc99b20ddd38bd26241 Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Thu, 12 Jun 2014 11:21:36 +0200 Subject: [PATCH] compiling cluster before tests --- source/cluster/wham/src-M/COMMON.CHAIN | 4 +++ .../wham/src-M/include_unres/COMMON.INTERACT | 2 ++ .../wham/src-M/include_unres/COMMON.SPLITELE | 2 ++ source/cluster/wham/src-M/parmread.F | 6 ++-- source/cluster/wham/src-M/readpdb.f | 33 +++++++++++++++----- source/cluster/wham/src-M/readrtns.F | 1 + 6 files changed, 37 insertions(+), 11 deletions(-) create mode 100644 source/cluster/wham/src-M/include_unres/COMMON.SPLITELE diff --git a/source/cluster/wham/src-M/COMMON.CHAIN b/source/cluster/wham/src-M/COMMON.CHAIN index d3f4c54..03b65c5 100644 --- a/source/cluster/wham/src-M/COMMON.CHAIN +++ b/source/cluster/wham/src-M/COMMON.CHAIN @@ -10,3 +10,7 @@ & chain_rep(3,maxres2+2,maxsym), nsup,nstart_sup, & nstart_seq, & nend_sup, chain_length,tabperm(maxperm,maxsym) + double precision boxxsize,boxysize,boxzsize,enecut,sscut,sss, + &sssgrad + common /box/ boxxsize,boxysize,boxzsize,enecut,sscut,sss,sssgrad + diff --git a/source/cluster/wham/src-M/include_unres/COMMON.INTERACT b/source/cluster/wham/src-M/include_unres/COMMON.INTERACT index 650af0d..0db8895 100644 --- a/source/cluster/wham/src-M/include_unres/COMMON.INTERACT +++ b/source/cluster/wham/src-M/include_unres/COMMON.INTERACT @@ -20,7 +20,9 @@ C 12/1/95 Array EPS included in the COMMON block. & eps_scp(ntyp,2),rscp(ntyp,2),eps_orig(ntyp,ntyp) c 12/5/03 modified 09/18/03 Bond stretching parameters. double precision vbldp0,vbldsc0,akp,aksc,abond0,distchainmax + &,vbldpDUM integer nbondterm common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp, & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp), & distchainmax,nbondterm(ntyp) + &,vbldpDUM diff --git a/source/cluster/wham/src-M/include_unres/COMMON.SPLITELE b/source/cluster/wham/src-M/include_unres/COMMON.SPLITELE new file mode 100644 index 0000000..a2f0447 --- /dev/null +++ b/source/cluster/wham/src-M/include_unres/COMMON.SPLITELE @@ -0,0 +1,2 @@ + double precision r_cut,rlamb + common /splitele/ r_cut,rlamb diff --git a/source/cluster/wham/src-M/parmread.F b/source/cluster/wham/src-M/parmread.F index f02e1a2..7adfb30 100644 --- a/source/cluster/wham/src-M/parmread.F +++ b/source/cluster/wham/src-M/parmread.F @@ -34,8 +34,8 @@ C Assign virtual-bond length vblinv=1.0D0/vbl vblinv2=vblinv*vblinv #ifdef CRYST_BOND - read (ibond,*) vbldp0,akp - do i=1,ntyp + read (ibond,*) vbldp0,vbldpdum,akp + do i=1,ntyp nbondterm(i)=1 read (ibond,*) vbldsc0(1,i),aksc(1,i) dsc(i) = vbldsc0(1,i) @@ -46,7 +46,7 @@ C Assign virtual-bond length endif enddo #else - read (ibond,*) ijunk,vbldp0,akp,rjunk + read (ibond,*) ijunk,vbldp0,vbldpdum,akp,rjunk do i=1,ntyp read (ibond,*) nbondterm(i),(vbldsc0(j,i),aksc(j,i),abond0(j,i), & j=1,nbondterm(i)) diff --git a/source/cluster/wham/src-M/readpdb.f b/source/cluster/wham/src-M/readpdb.f index 725065a..d6742c6 100644 --- a/source/cluster/wham/src-M/readpdb.f +++ b/source/cluster/wham/src-M/readpdb.f @@ -22,7 +22,8 @@ C geometry. goto 10 else if (card(:3).eq.'TER') then C End current chain - ires_old=ires+1 + ires_old=ires+2 + itype(ires_old-1)=ntyp1 itype(ires_old)=ntyp1 ibeg=2 c write (iout,*) "Chain ended",ires,ishift,ires_old @@ -82,13 +83,29 @@ C system do i=2,nres-1 c write (iout,*) i,itype(i) if (itype(i).eq.ntyp1) then + if (itype(i+1).eq.ntyp1) then + c write (iout,*) "dummy",i,itype(i) - do j=1,3 - c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2 +C do j=1,3 +C c(j,i)=((c(j,i-1)+c(j,i+1))/2+2*c(j,i-1)-c(j,i-2))/2 c c(j,i)=(c(j,i-1)+c(j,i+1))/2 - dc(j,i)=c(j,i) - enddo - endif +C dc(j,i)=c(j,i) +C enddo + do j=1,3 + dcj=(c(j,i-2)-c(j,i-3))/2.0 + c(j,i)=c(j,i-1)+dcj + c(j,nres+i)=c(j,i) + enddo +C endif !unres_pdb + else !itype(i+1).eq.ntyp1 + do j=1,3 + dcj=(c(j,i+3)-c(j,i+2))/2.0 + c(j,i)=c(j,i+1)-dcj + c(j,nres+i)=c(j,i) + enddo +C endif !unres_pdb + endif !itype(i+1).eq.ntyp1 + endif !itype.eq.ntyp1 enddo C Calculate the CM of the last side chain. call sccenter(ires,iii,sccor) @@ -98,7 +115,7 @@ C Calculate the CM of the last side chain. nres=nres+1 itype(nres)=ntyp1 do j=1,3 - dcj=c(j,nres-2)-c(j,nres-3) + dcj=(c(j,nres-2)-c(j,nres-3))/2.0 c(j,nres)=c(j,nres-1)+dcj c(j,2*nres)=c(j,nres) enddo @@ -116,7 +133,7 @@ C Calculate the CM of the last side chain. nsup=nsup-1 nstart_sup=2 do j=1,3 - dcj=c(j,4)-c(j,3) + dcj=(c(j,4)-c(j,3))/2.0 c(j,1)=c(j,2)-dcj c(j,nres+1)=c(j,1) enddo diff --git a/source/cluster/wham/src-M/readrtns.F b/source/cluster/wham/src-M/readrtns.F index f29d6f7..936cb42 100644 --- a/source/cluster/wham/src-M/readrtns.F +++ b/source/cluster/wham/src-M/readrtns.F @@ -15,6 +15,7 @@ C include 'COMMON.FFIELD' include 'COMMON.FREE' include 'COMMON.INTERACT' + include "COMMON.SPLITELE" character*320 controlcard,ucase #ifdef MPL include 'COMMON.INFO' -- 1.7.9.5