resolving merge conflicts

diff --git a/.gitignore b/.gitignore
index 4c3f4f2..d5a15a6 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -1,9 +1,3 @@
-<<<<<<< HEAD
-*.[oa] 
-*~
-*.swp
-*.[eo][0-9][0-9][0-9][0-9]*
-=======
 # ignore compiled stuff
 *.[oa]
 
@@ -11,6 +5,8 @@
 *.swp
 *~
 
+# ignore PBS output and error files
+*.[eo][0-9][0-9][0-9][0-9]*
 
 # ignore build dir
 build/
@@ -21,4 +17,3 @@ mapcheck/
 run/
 sympcheck/
 
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1

diff --git a/examples/unres/MD/ff_gab/1L2Y_minim.inp b/examples/unres/MD/ff_gab/1L2Y_minim.inp
index a770a21..2830886 100644 (file)
--- a/examples/unres/MD/ff_gab/1L2Y_minim.inp
+++ b/examples/unres/MD/ff_gab/1L2Y_minim.inp
@@ -1,11 +1,6 @@
 1L2Y
-<<<<<<< HEAD
 SEED=-3059743 REFSTR PDBREF MINIMIZE
 
-=======
-SEED=-3059743 PDBREF ENE
-maxmin=1000
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
 WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873            &
 WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000    &

diff --git a/source/cluster/wham/src/DIMENSIONS.COMPAR b/source/cluster/wham/src/DIMENSIONS.COMPAR
index f5d44d1..08e2231 100644 (file)
--- a/source/cluster/wham/src/DIMENSIONS.COMPAR
+++ b/source/cluster/wham/src/DIMENSIONS.COMPAR
@@ -2,14 +2,6 @@
 *
 * Array dimensions for level-based conformation comparison program:
 *
-<<<<<<< HEAD
-=======
-* Max. number of conformations in the data set.
-*
-      integer maxconf
-      PARAMETER (MAXCONF=maxstr_proc)
-*
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
 * Max. number levels of comparison
 *
       integer maxlevel

diff --git a/source/cluster/wham/src/include_unres/COMMON.INTERACT b/source/cluster/wham/src/include_unres/COMMON.INTERACT
index 2545afb..23bfd42 100644 (file)
--- a/source/cluster/wham/src/include_unres/COMMON.INTERACT
+++ b/source/cluster/wham/src/include_unres/COMMON.INTERACT
@@ -19,15 +19,7 @@ C 12/1/95 Array EPS included in the COMMON block.
      & r0d(ntyp,2),rpp(2,2),epp(2,2),elpp6(2,2),elpp3(2,2),
      & eps_scp(20,2),rscp(20,2),eps_orig(ntyp,ntyp)
 c 12/5/03 modified 09/18/03 Bond stretching parameters.
-<<<<<<< HEAD
       double precision vbldp0,vbldsc0,akp,aksc,abond0
       integer nbondterm
       common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp,
      & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),nbondterm(ntyp)
-=======
-      double precision vbldp0,vbldsc0,akp,aksc,abond0,distchainmax
-      integer nbondterm
-      common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp,
-     & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),
-     & distchainmax,nbondterm(ntyp)
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1

diff --git a/source/cluster/wham/src/include_unres/COMMON.SBRIDGE b/source/cluster/wham/src/include_unres/COMMON.SBRIDGE
index 2848b61..7bba010 100644 (file)
--- a/source/cluster/wham/src/include_unres/COMMON.SBRIDGE
+++ b/source/cluster/wham/src/include_unres/COMMON.SBRIDGE
@@ -1,5 +1,4 @@
       double precision ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,dhpb,
-<<<<<<< HEAD
      & dhpb1,forcon,weidis
       integer ns,nss,nfree,iss,ihpb,jhpb,nhpb,link_start,link_end,
      & ibecarb
@@ -7,13 +6,5 @@
      &  nfree,iss(maxss)
       common /links/ dhpb(maxdim),dhpb1(maxdim),forcon(maxdim),
      & ihpb(maxdim),jhpb(maxdim),ibecarb(maxdim),nhpb
-=======
-     & forcon,weidis
-      integer ns,nss,nfree,iss,ihpb,jhpb,nhpb,link_start,link_end
-      common /sbridge/ ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,ns,nss,
-     &  nfree,iss(maxss)
-      common /links/ dhpb(maxdim),forcon(maxdim),ihpb(maxdim),
-     & jhpb(maxdim),nhpb
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
       common /restraints/ weidis
       common /links_split/ link_start,link_end

diff --git a/source/cluster/wham/src/include_unres/COMMON.TORSION b/source/cluster/wham/src/include_unres/COMMON.TORSION
index 957dcff..8a12451 100644 (file)
--- a/source/cluster/wham/src/include_unres/COMMON.TORSION
+++ b/source/cluster/wham/src/include_unres/COMMON.TORSION
@@ -4,13 +4,8 @@ C Torsional constants of the rotation about virtual-bond dihedral angles
       common/torsion/v0(maxtor,maxtor),v1(maxterm,maxtor,maxtor),
      &    v2(maxterm,maxtor,maxtor),vlor1(maxlor,maxtor,maxtor),
      &    vlor2(maxlor,maxtor,maxtor),vlor3(maxlor,maxtor,maxtor),
-<<<<<<< HEAD
      &    itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),nlor(maxtor,maxtor) 
      &    ,nterm_old
-=======
-     &    itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),
-     &    nlor(maxtor,maxtor),nterm_old
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
 C 6/23/01 - constants for double torsionals
       double precision v1c,v1s,v2c,v2s
       integer ntermd_1,ntermd_2

diff --git a/source/unres/src_MD/cinfo.f b/source/unres/src_MD/cinfo.f
index b54ec8c..755efb0 100644 (file)
--- a/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@ -1,13 +1,4 @@
 C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-<<<<<<< HEAD
-C 2 5 66
-      subroutine cinfo
-      include 'COMMON.IOUNITS'
-      write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 2.5 build 66'
-      write(iout,*)'compiled Thu Jun 14 06:40:11 2012'
-      write(iout,*)'compiled by adam@matrix.chem.cornell.edu'
-=======
 C 2 5 295
       subroutine cinfo
       include 'COMMON.IOUNITS'
@@ -15,21 +6,15 @@ C 2 5 295
       write(iout,*)'Version 2.5 build 295'
       write(iout,*)'compiled Mon Jun 18 05:08:20 2012'
       write(iout,*)'compiled by aks255@matrix.chem.cornell.edu'
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
       write(iout,*)'OS name:    Linux '
       write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
       write(iout,*)'OS version:',
      & ' #1 SMP Tue May 3 09:23:03 UTC 2011 '
       write(iout,*)'flags:'
-<<<<<<< HEAD
-      write(iout,*)'FC = ifort'
-      write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include'
-=======
       write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
       write(iout,*)'FC= ifort'
       write(iout,*)'OPT =  -g -ip -w -CB '
       write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include '
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
       write(iout,*)'FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...'
       write(iout,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include'
       write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report ...'

diff --git a/source/xdrfpdb/src/xdrf2ang.f b/source/xdrfpdb/src/xdrf2ang.f
index f1c8472..763a945 100644 (file)
--- a/source/xdrfpdb/src/xdrf2ang.f
+++ b/source/xdrfpdb/src/xdrf2ang.f
@@ -14,11 +14,7 @@
       character*8 onethree,cfreq
       character*8 ucase
       external ucase
-<<<<<<< HEAD
       logical oneletter,iblnk
-=======
-      logical oneletter, iblnk
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
       integer rescode
       external rescode
       

diff --git a/source/xdrfpdb/src/xdrf2pdb-m.F b/source/xdrfpdb/src/xdrf2pdb-m.F
index 1fbf5af..61893ef 100644 (file)
--- a/source/xdrfpdb/src/xdrf2pdb-m.F
+++ b/source/xdrfpdb/src/xdrf2pdb-m.F
@@ -13,11 +13,7 @@
       character*3 licz
       character*8 ucase
       external ucase
-<<<<<<< HEAD
       logical oneletter,iblnk
-=======
-      logical oneletter, iblnk
->>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
       integer rescode
       external rescode