[gmx-users] prodrg

[Justin A. Lemkul]

Bhawana Gupta wrote:
> hello everyone,
>  
> Pls tell me whether we can use PRODRG server only for generating 
> peptides with unusual amino acid through JME or it can be used for the 
> peptides having usual amino acid.

PRODRG is most useful in obtaining topologies for small molecules.  You might 
use it to get the initial topology for an unusual amino acid, but you would 
probably be best to translate that topology into an .rtp file for yourself.

Be aware that the charges and charge groups generated by PRODRG typically 
require refinement and thorough validation of the parameters.

> whether it is necessary to use pdb2gmx for peptide containing usual 
> amino acid or we can do it with PRODRG server also.
>  

Well, you could write your topology by hand, if you really wanted to :)  But 
pdb2gmx makes life quite simple for generating topologies of proteins and peptides.

-Justin

> Pls help me out.
>  
> Bhawana
> 
> 
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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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