[gmx-users] Issue regarding MN+2
zebamir85 at gmail.com
Fri Dec 29 16:39:50 CET 2017
Thanks Dr. Justin.
I didn't add this stuff by my own.
I have created Mn+2 topology by simple pdb2gmx command.
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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users