I just copied the value from the other carbon types (1.352 I think?). CS
is a pyrimidine type from the RNA forcefield (the C5 and C6 carbons are
this type). Is there a reason this is not on the current list?
It looks like the error I got was the Python equivalent of a segfault.
Brian
On 08/28/2014 06:23 PM, Pengfei Li wrote:
> 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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>
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Received on Thu Aug 28 2014 - 17:00:06 PDT
