From 2900dbb2e7e1c992d8603e52c0d080ee009318c2 Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Fri, 22 Dec 2017 13:25:50 +0100 Subject: [PATCH] xdrf2pdb D amino --- source/xdrfpdb/src-M/COMMON.NAMES | 2 +- source/xdrfpdb/src-M/DIMENSIONS | 2 +- source/xdrfpdb/src-M/arcos.f | 2 +- source/xdrfpdb/src-M/geomout.F | 10 +++++----- source/xdrfpdb/src-M/nazwy.f | 11 +++++++++-- source/xdrfpdb/src-M/rescode.f | 4 ++-- source/xdrfpdb/src-M/xdrf2pdb.F | 4 ++-- 7 files changed, 21 insertions(+), 14 deletions(-) diff --git a/source/xdrfpdb/src-M/COMMON.NAMES b/source/xdrfpdb/src-M/COMMON.NAMES index e6f926b..1c85c4f 100644 --- a/source/xdrfpdb/src-M/COMMON.NAMES +++ b/source/xdrfpdb/src-M/COMMON.NAMES @@ -1,6 +1,6 @@ character*3 restyp character*1 onelet - common /names/ restyp(ntyp+1),onelet(ntyp+1) + common /names/ restyp(-ntyp1:ntyp1),onelet(-ntyp1:ntyp1) character*10 ename,wname integer nprint_ene,print_order common /namterm/ ename(n_ene),wname(n_ene),nprint_ene, diff --git a/source/xdrfpdb/src-M/DIMENSIONS b/source/xdrfpdb/src-M/DIMENSIONS index 32a8ae5..43e77a2 100644 --- a/source/xdrfpdb/src-M/DIMENSIONS +++ b/source/xdrfpdb/src-M/DIMENSIONS @@ -38,7 +38,7 @@ C Max. number of contacts per residue parameter (maxconts=maxres) C Number of AA types (at present only natural AA's will be handled integer ntyp,ntyp1 - parameter (ntyp=20,ntyp1=ntyp+1) + parameter (ntyp=24,ntyp1=ntyp+1) C Max. number of types of dihedral angles & multiplicity of torsional barriers C and the number of terms in double torsionals integer maxtor,maxterm,maxlor,maxtermd_1,maxtermd_2 diff --git a/source/xdrfpdb/src-M/arcos.f b/source/xdrfpdb/src-M/arcos.f index afc6724..69810ea 100644 --- a/source/xdrfpdb/src-M/arcos.f +++ b/source/xdrfpdb/src-M/arcos.f @@ -2,7 +2,7 @@ implicit real*8 (a-h,o-z) include 'COMMON.GEO' IF (DABS(X).LT.1.0D0) GOTO 1 - ARCOS=0.5D0*(PI-DSIGN(1.0D0,X)*PI) + ARCOS=0.5D0*(PI+DSIGN(1.0D0,X)*PI) RETURN 1 ARCOS=DACOS(X) RETURN diff --git a/source/xdrfpdb/src-M/geomout.F b/source/xdrfpdb/src-M/geomout.F index e8101a2..e356fd2 100644 --- a/source/xdrfpdb/src-M/geomout.F +++ b/source/xdrfpdb/src-M/geomout.F @@ -94,7 +94,7 @@ c endif iatom=iatom+1 ica(i)=iatom iti=itype(i) - if (iti.eq.21) then + if (iti.eq.ntyp1) then ichain=ichain+1 ires=0 write (iunit,'(a)') 'TER' @@ -114,12 +114,12 @@ c endif enddo write (iunit,'(a)') 'TER' do i=nnt,nct-1 - if (itype(i).eq.21) cycle - if (itype(i).eq.10 .and. itype(i+1).ne.21) then + if (itype(i).eq.ntyp1) cycle + if (itype(i).eq.10 .and. itype(i+1).ne.ntyp1) then write (iunit,30) ica(i),ica(i+1) - else if (itype(i).ne.10 .and. itype(i+1).ne.21) then + else if (itype(i).ne.10 .and. itype(i+1).ne.ntyp1) then write (iunit,30) ica(i),ica(i+1),ica(i)+1 - else if (itype(i).ne.10 .and. itype(i+1).eq.21) then + else if (itype(i).ne.10 .and. itype(i+1).eq.ntyp1) then write (iunit,30) ica(i),ica(i)+1 endif enddo diff --git a/source/xdrfpdb/src-M/nazwy.f b/source/xdrfpdb/src-M/nazwy.f index 9f61cfb..d495120 100644 --- a/source/xdrfpdb/src-M/nazwy.f +++ b/source/xdrfpdb/src-M/nazwy.f @@ -4,10 +4,17 @@ include 'COMMON.NAMES' include 'COMMON.FFIELD' data restyp / + &'DD','DAU','DAI','DDB','DSM','DPR','DLY','DAR','DHI','DAS','DGL', + & 'DSG','DGN','DSN','DTH', + &'DYY','DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY','ZER', &'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR', - &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/ + &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','SME','DBZ', + &'AIB','ABU','D'/ data onelet / + &'z','z','z','z','z','p','k','r','h','d','e','n','q','s','t','g', + &'a','y','w','v','l','i','f','m','c','x', &'C','M','F','I','L','V','W','Y','A','G','T', - &'S','Q','N','E','D','H','R','K','P','X'/ + &'S','Q','N','E','D','H','R','K','P','z','z','z','z','X'/ + data potname /'LJ','LJK','BP','GB','GBV'/ end diff --git a/source/xdrfpdb/src-M/rescode.f b/source/xdrfpdb/src-M/rescode.f index 1fff9ec..efa6c5c 100644 --- a/source/xdrfpdb/src-M/rescode.f +++ b/source/xdrfpdb/src-M/rescode.f @@ -7,7 +7,7 @@ if (ione.eq.0) then - do i=1,ntyp1 + do i=-ntyp1,ntyp1 if (ucase(nam).eq.restyp(i)) then rescode=i return @@ -15,7 +15,7 @@ enddo else - do i=1,ntyp1 + do i=-ntyp1,ntyp1 if (nam(1:1).eq.onelet(i)) then rescode=i return diff --git a/source/xdrfpdb/src-M/xdrf2pdb.F b/source/xdrfpdb/src-M/xdrf2pdb.F index c87e9ff..503d7d7 100644 --- a/source/xdrfpdb/src-M/xdrf2pdb.F +++ b/source/xdrfpdb/src-M/xdrf2pdb.F @@ -88,9 +88,9 @@ endif open(9,file=pdbfile) nnt = 1 - if (itype(1).eq.21) nnt = 2 + if (itype(1).eq.ntyp1) nnt = 2 nct=nres - if (itype(nres).eq.21) nct = nres-1 + if (itype(nres).eq.ntyp1) nct = nres-1 print *,"nnt",nnt," nct",nct print *,"file",arg call xdrfopen(ixdrf,arg, "r", iret) -- 1.7.9.5