I have a simple prmtop file for an RNA system with a bound Mg that I want
to convert from a normal 12-6 to the new 12-6-4 potential. I tried using
the following parmed.py commands:
>>parmed.py prmtop
add12_6_4 :MG watermodel TIP4PEW
and got the following error/warning:
Adding Lennard-Jones C-coefficient for 12-6-4 potential. Polarizabilities
read from
[/home/radakb/devel/git/Programs/Amber11/dat/leap/parm/lj_1264_pol.dat].
Using default C4 parameters for water model [TIP4PEW].
***********************************************************
The selected metal ion is Mg
Action add12_6_4 failed
LJ12_6_4Error: Could not find parameters for ATOM_TYPE CS
So I tried modifying "lj_1264_pol.dat" by adding the CS type. Presumably
this was omitted because CS and Cs could cause trouble (so I also deleted
the Cs line because I don't really need that for now)? In any event I now
get this error:
The selected metal ion is Mg
Traceback (most recent call last):
File "/home/radakb/devel/git/Programs/Amber11/bin/parmed.py", line 161,
in <module>
parmed_commands.cmdloop()
File "/usr/lib64/python2.7/cmd.py", line 142, in cmdloop
stop = self.onecmd(line)
File "/usr/lib64/python2.7/cmd.py", line 221, in onecmd
return func(arg)
File "<string>", line 1, in <lambda>
File
"/u2/home2/radakb2/git/Programs/Amber11/bin/ParmedTools/parmed_cmd.py",
line 141, in _normaldo
action.execute()
File
"/u2/home2/radakb2/git/Programs/Amber11/bin/ParmedTools/ParmedActions.py",
line 2857, in execute
self.tunfactor)):
File "/u2/home2/radakb2/git/Programs/Amber11/bin/ParmedTools/add1264.py",
line 119, in params1264
atomtypej = amberatomtypelist2[j]
IndexError: list index out of range
Which is a bit more opaque to me. Any ideas?
Thanks,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
====================================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 28 2014 - 13:00:03 PDT
