AW: [gmx-users] protonation state with pdb2gmx

[Justin A. Lemkul]

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

If the C-terminus bears the charge, then simply choose COO- as your C-terminus.

If the sidechain is somehow deprotonated, then you have to come up with the 
parameters for yourself.

-Justin

> ________________________________________ 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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-- 
========================================

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

========================================