[gmx-users] Parametrisation of the heteroatomic pdb

[Justin A. Lemkul]

James Starlight wrote:
> Justin?
> 
> So As I understood the aminoacids.rtp of current force field must 
> include topology for such caps.
> 

Yes.  Any residue whatsoever that you wish to process with pdb2gmx must be 
present in an .rtp file.

> But for example If I have only topology on such groups for another ff 
> could I include it to the amber FF? If no where I could find such topology ?
> 

Do not mix and match force fields.  Even if you can hack it into working, the 
results will be absolute garbage.  If you need a topology for a specific force 
field, refer to the parameterization link I posted before.  Deriving parameters 
for new residues in an existing force field is a task that may take weeks or 
months to do properly and hence is considered an expert topic.  I have nothing 
more to contribute on that issue.  The archives are filled with tips and 
discussions on how to go about such things.

-Justin

> 
> James
> 
> 2011/10/28 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     James Starlight wrote:
> 
> 
>         I understood that but how I can add that groups to termi of the
>         bowh of my chains ?
> 
>         I've tried by -ter but pdb2gmx didnt ask me for the addition of
>         the CAPS. May be Amber ff didnt support this feature ?
> 
> 
>     pdb2gmx does not build things that aren't there.  Your input
>     coordinate file needs to have the capping groups present, with all
>     atoms named as the .rtp entries expect them, hence the suggestion to
>     investigate the [ACE] and [NME] directives.
> 
>     -Justin
> 
> 
> 
>         James
> 
> 
>            You have to build capping groups onto the termini.  See, for
>            instance the [ACE] and [NME] groups in the .rtp file.
> 
>            -Justin
> 
> 
> 
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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-- 
========================================

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

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