[gmx-users] Issue regarding MN+2
jalemkul at vt.edu
Fri Dec 29 17:17:27 CET 2017
On 12/29/17 10:39 AM, Amir Zeb wrote:
> Thanks Dr. Justin.
> I didn't add this stuff by my own.
> I have created Mn+2 topology by simple pdb2gmx command.
Someone hacked your files and added it at some point. None of the
releases of the C36 port that I have ever made had contained Mn2+
parameters. There are CHARMM-compatible parameters that could be added
as part of a larger metal parameter set, but they've never been included
in the port.
Regardless, that's what you need to do - add the correct sigma and
epsilon values to ffnonbonded.itp for the MN atom type.
> On Dec 30, 2017 12:21 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>> On 12/29/17 10:11 AM, Amir Zeb wrote:
>>> Hello dear gromacs users,
>>> I want to simulate a protein which has two Mn+2 ions as co-factor.
>>> Till the solvation, I could prepare the system, but at neutralization
>>> grompp gives me this fatal error.
>>> Fatal error:
>>> Atomtype MN not found
>>> My system has this topology for Mn+2:
>>> [ moleculetype ]
>>> ; Name nrexcl
>>> Other_chain_C2 3
>>> [ atoms ]
>>> ; nr type resnr residue atom cgnr charge mass typeB
>>> chargeB massB
>>> ; residue 501 MN2 rtp MN q +2.0
>>> 1 MN 501 MN2 MN 1 2 54.94 ;
>>> qtot 2
>>> ; residue 502 MN2 rtp MN q +2.0
>>> 2 MN 502 MN2 MN 2 2 54.94 ;
>>> qtot 4
>>> And the Mn+2 has this configuration:
>>> 501MN2 MN 4551 5.405 5.564 2.987
>>> 502MN2 MN 4552 5.582 5.590 3.497
>>> I have used Charmm36 ff, and the gromacs version is 5.0.6
>>> Please let me know how can I fix this issue?
>> This is not a standard CHARMM atom type - did you add it yourself? If so,
>> what was the source of the parameters? It looks like you have a residue
>> defined in the .rtp, hence pdb2gmx wrote the topology, but you don't
>> actually have parameters assigned for the atom type in ffnonbonded.itp.
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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