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#! /bin/sh /usr/share/dpatch/dpatch-run
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## 02_cyclic_protein.dpatch by LI Daobing <lidaobing@gmail.com>
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##
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## All lines beginning with `## DP:' are a description of the patch.
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## DP: fix a bug when generate cyclic peptide, sometimes the atom type will
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## DP: have some error.
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@DPATCH@
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diff -urNad tinker~/source/protein.f tinker/source/protein.f
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--- tinker~/source/protein.f 2004-09-08 06:37:36.000000000 +0800
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+++ tinker/source/protein.f 2007-05-19 14:49:10.000000000 +0800
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@@ -429,7 +429,7 @@
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& ni(i),cai(i),ci(i),0)
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call zatom (hatyp(k),1.11d0,109.5d0,107.9d0,
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& cai(i),ni(i),ci(i),-chiral(i))
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- call proside (resname,i,cai(i),ni(i),ci(i))
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+ call proside (resname,i,cai(i),ni(i),ci(i), cyclic)
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c
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c build the first residue as an N-terminal formyl group
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c
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@@ -479,7 +479,7 @@
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& ni(i),cai(i),ci(i),0)
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call zatom (hantyp(k),1.11d0,109.5d0,107.9d0,
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& cai(i),ni(i),ci(i),-chiral(i))
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- call proside (resname,i,cai(i),ni(i),ci(i))
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+ call proside (resname,i,cai(i),ni(i),ci(i), cyclic)
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c
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c build the first residue as a pyroglutamic acid
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c
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@@ -502,7 +502,7 @@
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& ni(i),cai(i),ci(i),0)
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call zatom (hantyp(k),1.11d0,109.5d0,107.9d0,
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& cai(i),ni(i),ci(i),-chiral(i))
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- call proside (resname,i,cai(i),ni(i),ci(i))
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+ call proside (resname,i,cai(i),ni(i),ci(i), cyclic)
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c
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c build the first residue for all other standard amino acids
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c
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@@ -529,7 +529,7 @@
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& ni(i),cai(i),n-2,-1)
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call zatom (hantyp(k),1.11d0,109.5d0,107.9d0,
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& cai(i),ni(i),ci(i),-chiral(i))
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- call proside (resname,i,cai(i),ni(i),ci(i))
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+ call proside (resname,i,cai(i),ni(i),ci(i), cyclic)
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end if
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c
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c build atoms for residues in the middle of the chain
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@@ -552,7 +552,7 @@
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& ni(i),cai(i),ci(i),0)
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call zatom (hatyp(k),1.11d0,109.5d0,107.9d0,
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& cai(i),ni(i),ci(i),-chiral(i))
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- call proside (resname,i,cai(i),ni(i),ci(i))
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+ call proside (resname,i,cai(i),ni(i),ci(i), cyclic)
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end do
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c
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c set the number and type of the last residue
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@@ -580,7 +580,7 @@
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& ni(i),cai(i),ci(i),0)
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call zatom (hatyp(k),1.11d0,109.5d0,107.9d0,
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& cai(i),ni(i),ci(i),-chiral(i))
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- call proside (resname,i,cai(i),ni(i),ci(i))
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+ call proside (resname,i,cai(i),ni(i),ci(i), cyclic)
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c
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c build the last residue as a C-terminal amide
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c
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@@ -627,7 +627,7 @@
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& ni(i),cai(i),ci(i),0)
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call zatom (hactyp(k),1.11d0,109.5d0,107.9d0,
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& cai(i),ni(i),ci(i),-chiral(i))
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- call proside (resname,i,cai(i),ni(i),ci(i))
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+ call proside (resname,i,cai(i),ni(i),ci(i), cyclic)
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end if
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call zatom (octyp(k),1.25d0,117.0d0,psi(i),
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& ci(i),cai(i),ni(i),0)
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@@ -655,24 +655,26 @@
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c cai atom number of alpha carbon in residue i
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c ni atom number of amide nitrogen in residue i
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c ci atom number of carbonyl carbon in residue i
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+c cyclic is cyclic?
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c
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c
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- subroutine proside (resname,i,cai,ni,ci)
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+ subroutine proside (resname,i,cai,ni,ci,cyclic)
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implicit none
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include 'sizes.i'
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include 'atoms.i'
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include 'phipsi.i'
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include 'sequen.i'
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integer i,cai,ni,ci
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+ logical cyclic
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character*3 resname
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c
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c
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c glycine residue (GLY)
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c
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if (resname .eq. 'GLY') then
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- if (i .eq. 1) then
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+ if (i .eq. 1 .and. .not. cyclic) then
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call zatom (355,1.11d0,109.5d0,107.9d0,cai,ni,ci,chiral(i))
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- else if (i .eq. nseq) then
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+ else if (i .eq. nseq .and. .not. cyclic) then
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call zatom (506,1.11d0,109.5d0,107.9d0,cai,ni,ci,chiral(i))
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else
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call zatom (6,1.11d0,109.5d0,107.9d0,cai,ni,ci,chiral(i))
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@@ -786,7 +788,7 @@
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else if (resname .eq. 'PRO') then
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call zatom (101,1.54d0,107.0d0,109.5d0,cai,ni,ci,chiral(i))
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call zatom (103,1.54d0,107.0d0,chi(1,i),n-1,cai,ni,0)
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- if (i .eq. 1) then
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+ if (i .eq. 1 .and. .not. cyclic) then
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call zatom (410,1.54d0,107.0d0,chi(2,i),n-1,n-2,cai,0)
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else
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call zatom (105,1.54d0,107.0d0,chi(2,i),n-1,n-2,cai,0)
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@@ -796,7 +798,7 @@
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call zatom (102,1.11d0,109.4d0,109.4d0,n-4,cai,n-3,-1)
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call zatom (104,1.11d0,109.4d0,109.4d0,n-4,n-5,n-3,1)
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call zatom (104,1.11d0,109.4d0,109.4d0,n-5,n-6,n-4,-1)
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- if (i .eq. 1) then
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+ if (i .eq. 1 .and. .not. cyclic) then
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call zatom (411,1.11d0,109.4d0,109.4d0,n-5,n-6,ni,1)
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call zatom (411,1.11d0,109.4d0,109.4d0,n-6,n-7,ni,-1)
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else
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@@ -1068,9 +1070,9 @@
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c unknown residue (UNK)
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c
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else if (resname .eq. 'UNK') then
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- if (i .eq. 1) then
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+ if (i .eq. 1 .and. .not. cyclic) then
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call zatom (355,1.11d0,109.5d0,107.9d0,cai,ni,ci,chiral(i))
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- else if (i .eq. nseq) then
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+ else if (i .eq. nseq .and. .not. cyclic) then
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call zatom (506,1.11d0,109.5d0,107.9d0,cai,ni,ci,chiral(i))
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else
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call zatom (6,1.11d0,109.5d0,107.9d0,cai,ni,ci,chiral(i))
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