projects
/
unres.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
655daea
)
Commit 10/17/12 Adam
author
Adam Liwo
<jal47@matrix.chem.cornell.edu>
Wed, 17 Oct 2012 04:33:56 +0000
(
00:33
-0400)
committer
Adam Liwo
<jal47@matrix.chem.cornell.edu>
Wed, 17 Oct 2012 04:33:56 +0000
(
00:33
-0400)
bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe
patch
|
blob
|
history
bin/unres/MD/unres_ifort_single_GAB.exe
patch
|
blob
|
history
source/unres/src_CSA/readpdb.F
patch
|
blob
|
history
source/unres/src_CSA/readrtns_csa.F
patch
|
blob
|
history
source/unres/src_MD/readpdb.F
patch
|
blob
|
history
source/unres/src_MD/readrtns.F
patch
|
blob
|
history
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
(executable)
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
(executable)
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
(file)
--- 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)
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
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
(file)
--- 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
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
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
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
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
(file)
--- 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)
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
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
(file)
--- 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
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
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
& i,' after ',nsi,' trials'
endif
enddo
+C 10/03/12 Adam: Recalculate coordinates with new side chain positions
+ call chainbuild
endif
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.
endif
if (indpdb.eq.0) then
C Read sequence if not taken from the pdb file.