Hi Brian,
What is the polarizability parameter for CS atom type do you use? It may be because the
VDW parameter consistence caused this problem.
All the best,
Pengfei
On Aug 28, 2014, at 3:45 PM, Brian Radak <radak004.umn.edu> wrote:
> 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 :
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Received on Thu Aug 28 2014 - 15:30:02 PDT
