[gmx-users] generating topology for artificial residues

[Justin A. Lemkul]

Grange Hermitage wrote:
> Hi all,
>  
> What approach to use to generate a topology file for peptides which 
> include artificial residues such as serine with its sidechain extended 
> by two carbons to double bond with another such residue i.e.
> CA-CB-OG-C1-C3=C4-C2-OG-CB-CA
>  
> Also I need to generate a topology for another type of 
> artificial peptide which includes beta-3 residues (C inserted in 
> mainchain between CA and C ).
>  
> Say I want to use a force field other than the 2 supported by the 
> PRODRG2.5 server.
>  
> I have tried to defining ff*.rtp residue definitions, but .top generated 
> by pdb2top are missing defaults essential for grompp (gb_ gd_). The 
> residue definitions have only [ atom ] specifications, allowing 
> the other sections to default as per the manual.
>  

Well, then the defaults don't apply for whatever you've tried to connect. 
Basically, check out the *bon.itp file for your force field and make sure the 
parameters that you think you are generating are actually there, and then check 
the naming you've given your atom types to make sure it is appropriate and 
compatible with the ones that the force field is expecting.

Without showing us what you've tried, it's difficult to diagnose.

-Justin

> thanks,
>    Grange.
>  
>   
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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