[gmx-users] C-terminus residue name in Gromos43a1

[Justin Lemkul]

On 2/24/14, 5:35 AM, Francesca Vitalini wrote:
> Dear Gromacs Users,
>
> does anybody know the residue name for the c-terminus NHMe in Gromos43a1. I
> tried NAC that works for GROMOS53 but it doesn't exist in the
> /gromos43a1.ff/aminoacids.rtp and there I couldn't find the correct name.
> However, it seems improbable that such a standard thing is not implemented
> by default.

It's not improbable at all; the force fields are updated individually, so 
changes in one may not be reflected in the others.

> If anyone has previously used it, could you please let me know how to
> introduce it correctly in my pdb structure so that it is recognized by
> pdb2gmx?
>

It's fairly straightforward to use the 53A6 .rtp entry as a basis for 43A1.  The 
only difference will be the charges on N and H that need to be changed to agree 
with 43A1 backbone charges.

-Justin

> So far I get this error message
>
> Program pdb2gmx, VERSION 4.5.5
> Source code file: /tmp/build/gromacs-4.5.5/src/kernel/resall.c, line: 581
>
> Fatal error:
> Residue 'NAC' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Thank you very much,
>
> Francesca
>

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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