Hi Brian,
On Aug 29, 2014, at 9:39 AM, Brian Radak <radak004.umn.edu> wrote:
> 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
Here you loaded the frcmod.ionslrcm_hfe_tip3p, maybe the frcmod.ionslm_1264_tip3p is actually you want? That is specified for 12-6-4 nonbonded model. ; )
> 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.
That may cause the problem. It seems the problem is that you have an atom type number
which is bigger than the biggest number of the atom type index. Can you send
me the prmtop file you tried to add the C4 terms before?
> I also have a few protonated RNA residues, if
> that is an issue.
>
This may be fine.
> 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
>
All the best,
Pengfei
>
>
> 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 :
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Received on Fri Aug 29 2014 - 08:00:03 PDT
