From fd9626b06479a4107300c3237a392fdd9a8b28a3 Mon Sep 17 00:00:00 2001 From: Adam Liwo Date: Wed, 17 Oct 2012 00:33:56 -0400 Subject: [PATCH 1/1] Commit 10/17/12 Adam --- source/unres/src_CSA/readpdb.F | 3 +++ source/unres/src_CSA/readrtns_csa.F | 8 ++++++++ source/unres/src_MD/readpdb.F | 3 +++ source/unres/src_MD/readrtns.F | 8 ++++++++ 4 files changed, 22 insertions(+) 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. -- 1.7.9.5