[gmx-users] regarding simulation of peptide and protein complex

Javier Cerezo jcb1 at um.es
Thu Jul 14 09:22:16 CEST 2011

Hi Rashi

To me, it seems more reasonable to use "pdb2gmx" for every molecule that 
is supported by this utility (i.e. included in a rtp file) as it will be 
more likely to be FF-compliant (at least for the default rtp files) and 
thus compatible with your protein. PRODRG is, used with some cautions, a 
very nice tool for kind of non-standard ligands (as drugs) not included 
is such databases, but just for them.

If the starting PDB structure of your peptide is OK you would be able to 
run "pdb2gmx" properly. Just try it and see


El 14/07/11 08:39, rashi parihar escribió:
> Hello everyone..
> I have to do the simulation of protein and peptide complex.I want to 
> ask as for protein and ligand complex we have to create topology of 
> ligand using prodrg sever mostly.Now if ligand is peptide then I have 
> to build the topology of  peptide using pdb2gx  or anyother 
> means?Looking forward 4r reply!!
> -- 
> images[12]
> “Many Smiles Begin Because Of Another Smile . . . ."
> Regards,
> Rashi

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