AW: [gmx-users] protonation state with pdb2gmx

[Yamin, Peyman]

OH! And a (-1) Alanine I can never have since pdb2gmx has no option for that? It's my C-Terminus in the end! :-|


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Von: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] im Auftrag von Justin A. Lemkul [jalemkul at vt.edu]
Gesendet: Montag, 29. Juni 2009 16:53
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] protonation state with pdb2gmx

Yamin, Peyman wrote:
> Hello,
>
> with pdb2gmx I want to choose the protonation state of a GLN interactively.
> When I choose +1 protonation state, I get the following error: Residue 'QLN'
> not found in residue topology database. But the program has itself suggested
> the QLN as the name of this protonation state!!
>

Then you've chosen a force field for which the name QLN simply doesn't apply :)

In fact, the only force field with QLN is OPLS.

-Justin

> Would be pleased by your comments! cheers, Peyman
>
>
>
>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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