[gmx-users] fatal error in gromacs

[Justin Lemkul]

On 10/17/14 6:36 AM, Yaser Hosseini wrote:
> hi gromacs users
>
> when i want to run pdb2gmx command i got a fatal error that said :
>
> the residue from MN has lost.
>
> and i used all of force feild but i got this error how can i fix it and
> which one of force feild coomand can i use??
>

Mn is probably not supported by default in most force fields, but I know 
parameters exist that are compatible with AMBER force fields.  You'll have to 
add a residue in the .rtp file and nonbonded parameters in ffnonbonded.itp.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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