From: Adam Liwo <jal47@matrix.chem.cornell.edu>
Date: Wed, 17 Oct 2012 04:33:56 +0000 (-0400)
Subject: Commit 10/17/12 Adam
X-Git-Tag: v.3.2~68^2
X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=e35b804370a6a557a65f6426600850b530c33bd9

Commit 10/17/12 Adam
---

diff --git a/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe b/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe
index 50cc426..098d4e1 100755
Binary files a/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe and b/bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe differ
diff --git a/bin/unres/MD/unres_ifort_single_GAB.exe b/bin/unres/MD/unres_ifort_single_GAB.exe
index 228bcd7..df1e14c 100755
Binary files a/bin/unres/MD/unres_ifort_single_GAB.exe and b/bin/unres/MD/unres_ifort_single_GAB.exe differ
diff --git a/source/unres/src_CSA/readpdb.F b/source/unres/src_CSA/readpdb.F
index dacd12d..69ec3e1 100644
--- a/source/unres/src_CSA/readpdb.F
+++ b/source/unres/src_CSA/readpdb.F
@@ -258,6 +258,9 @@ c      endif
           enddo
           iti=itype(i)
           di=dist(i,nres+i)
+C 10/03/12 Adam: Correction for zero SC-SC bond length
+          if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+     &     di=dsc(itype(i))
           vbld(i+nres)=di
           if (itype(i).ne.10) then
             vbld_inv(i+nres)=1.0d0/di
diff --git a/source/unres/src_CSA/readrtns_csa.F b/source/unres/src_CSA/readrtns_csa.F
index 17b2165..9ab4510 100644
--- a/source/unres/src_CSA/readrtns_csa.F
+++ b/source/unres/src_CSA/readrtns_csa.F
@@ -455,6 +455,9 @@ c        print *,'Finished reading pdb data'
         call contact(.false.,ncont_ref,icont_ref,co)
 
         if (sideadd) then 
+C Following 2 lines for diagnostics; comment out if not needed
+         write (iout,*) "Before sideadd"
+         call intout
          if(me.eq.king.or..not.out1file)
      &    write(iout,*)'Adding sidechains'
          maxsi=1000
@@ -472,6 +475,11 @@ c              call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
           endif
          enddo
         endif  
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+        call chainbuild
+C Following 2 lines for diagnostics; comment out if not needed
+        write (iout,*) "After sideadd"
+        call intout
       endif
 
       if (indpdb.eq.0) then
diff --git a/source/unres/src_MD/readpdb.F b/source/unres/src_MD/readpdb.F
index 563941b..97e9aa8 100644
--- a/source/unres/src_MD/readpdb.F
+++ b/source/unres/src_MD/readpdb.F
@@ -260,6 +260,9 @@ c      endif
           enddo
           iti=itype(i)
           di=dist(i,nres+i)
+C 10/03/12 Adam: Correction for zero SC-SC bond length
+          if (itype(i).ne.10 .and. itype(i).ne.21. and. di.eq.0.0d0)
+     &     di=dsc(itype(i))
           vbld(i+nres)=di
           if (itype(i).ne.10) then
             vbld_inv(i+nres)=1.0d0/di
diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F
index 47850c2..6b0e362 100644
--- a/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@ -893,6 +893,9 @@ c        print *,'Finished reading pdb data'
         call contact(.false.,ncont_ref,icont_ref,co)
 
         if (sideadd) then 
+C Following 2 lines for diagnostics; comment out if not needed
+         write (iout,*) "Before sideadd"
+         call intout
          if(me.eq.king.or..not.out1file)
      &    write(iout,*)'Adding sidechains'
          maxsi=1000
@@ -909,7 +912,12 @@ c        print *,'Finished reading pdb data'
      &              i,' after ',nsi,' trials'
           endif
          enddo
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+         call chainbuild
         endif  
+C Following 2 lines for diagnostics; comment out if not needed
+        write (iout,*) "After sideadd"
+        call intout
       endif
       if (indpdb.eq.0) then
 C Read sequence if not taken from the pdb file.