projects
/
unres.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
73bfa34
)
changed SCCORPAR to shelly potentials in GAB & 12LY ff - UNRESInpGen.py
author
Dawid Jagiela
<lightnir@chem.univ.gda.pl>
Mon, 15 Apr 2013 11:38:26 +0000
(13:38 +0200)
committer
Dawid Jagiela
<lightnir@chem.univ.gda.pl>
Mon, 15 Apr 2013 11:38:26 +0000
(13:38 +0200)
source/pymol/UNRESInpGen.py
patch
|
blob
|
history
diff --git
a/source/pymol/UNRESInpGen.py
b/source/pymol/UNRESInpGen.py
index
e1252b5
..
ca8c516
100755
(executable)
--- a/
source/pymol/UNRESInpGen.py
+++ b/
source/pymol/UNRESInpGen.py
@@
-924,7
+924,13
@@
class UNRESInpGenerator(Toplevel):
'''
Writes the C-shell script needed to run UNRES calculations
'''
'''
Writes the C-shell script needed to run UNRES calculations
'''
- s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py\n#\n'
+ s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py v'+UNRESInpGen_version+' \n#\n'
+
+ s+='#--------------------------------------------------------------------\n'
+ s+='# Uncomment and set these variables to run MPI versions of UNRES\n'
+ s+='#setenv UNRES_ROOT /path/to/root/directory/of/unrespack\n'
+ s+='#setenv UNRES_BIN /path/to/unres_binary.exe\n'
+ s+='#--------------------------------------------------------------------\n'
# number of processors per energy
if self.OM1Val.get()=="MD":
# number of processors per energy
if self.OM1Val.get()=="MD":
@@
-970,7
+976,7
@@
class UNRESInpGenerator(Toplevel):
elif self.OM2Val.get()=="GAB":
s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k\n'
elif self.OM2Val.get()=="GAB":
s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k\n'
- s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
+ s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/sccor_pdb_shelly.dat\n'
elif self.OM2Val.get()=="E0G":
s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc\n'
elif self.OM2Val.get()=="E0G":
s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc\n'
@@
-978,7
+984,7
@@
class UNRESInpGenerator(Toplevel):
elif self.OM2Val.get()=="1L2Y_1LE1":
s+='setenv BONDPAR $DD/bond_AM1.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm\n'
s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_$POT.parm\n'
elif self.OM2Val.get()=="1L2Y_1LE1":
s+='setenv BONDPAR $DD/bond_AM1.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm\n'
s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_$POT.parm\n'
- s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
+ s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/sccor_pdb_shelly.dat\n'
elif self.OM2Val.get()=="Custom":
s+='setenv BONDPAR $DD/.parm\nsetenv THETPAR $DD/.parm\nsetenv ROTPAR $DD/.parm\n'
s+='setenv TORPAR $DD/.parm\nsetenv TORDPAR $DD/.parm\nsetenv SIDEPAR $DD/.parm\n'
elif self.OM2Val.get()=="Custom":
s+='setenv BONDPAR $DD/.parm\nsetenv THETPAR $DD/.parm\nsetenv ROTPAR $DD/.parm\n'
s+='setenv TORPAR $DD/.parm\nsetenv TORDPAR $DD/.parm\nsetenv SIDEPAR $DD/.parm\n'