[gmx-users] Parametrisation of the heteroatomic pdb

[Justin A. Lemkul]

James Starlight wrote:
> Justin,
> 
> Could you tell me another alternative ways to replace existing cap 
> groups in my pdb besides xleap ? ( I've had  many problems with the 
> pdb's processed by this soft). Also I've tried to make topology for the 
> non-standart caps by PRODRG but I also have some problems with such 
> parametrisation.
> 

Unless you describe your problems, there's very little anyone can or will try to 
do to help you.  I've never had a problem with an xleap coordinate file, so I 
can't offer you any additional guidance with that.  Otherwise, there are dozens 
of programs that are capable of drawing molecules or editing files.  See, for 
instance:

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

-Justin

> 
> Also I've not found suitable topology for some D-isomers ( it's strange 
> that parametriation for such typical non-standart residues is absent in 
> all force fields ). As I understood I cant use topology of L-analogs for 
> the parametrisation of such D-forms because I dont know suitable 
> parameters for dihedrals for instance.
> Have someone pre-built parameters for the D-aa for Gromos or Charmm 
> force field?
> 
> 
> Thanks,
> 
> James
> 
> 2011/10/29 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     James Starlight wrote:
> 
>         Justin, hello!
> 
>         Could you tell me what exactly program from the Amber tools
>         package you've used for the KALP peptide preparation e.g for
>         capping ?
> 
> 
>     xleap
> 
>     At this point, please start a new thread for your questions, as
>     these topics are completely unrelated to where you started.
> 
>     -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

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