Update.
So a colleague and I tried to create a minimum working example of this
by creating a simple prmtop in tleap:
source learpc.ff14SB
loadamberparams frcmod.ionslrcm_hfe_tip3p
mol = UN
addions mol MG 1
saveamberparm mol foo.parm7 foo.rst7
quit
and then the same parmed.py commands
>parmed.py foo.parm7
add12_6_4 :MG
And this works as expected. I think there may be a subtle difference in
the prmtop I am using. First I have loaded my own LJ parameters for Mg
and called the residue and atom name and type "MG", not Mg2+ as the
standard libraries now do. I also have a few protonated RNA residues, if
that is an issue.
Does this help find the problem at all? Is that fastest solution just to
remake my prmtop in this fashion via leap? I am not keeping a solvent
box or anything. I just want to use this structure for GB/PB/RISM
calculations.
Brian
On 08/28/2014 07:47 PM, Brian Radak wrote:
> 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 :
>>> ====================================================================
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Aug 29 2014 - 07:00:02 PDT
