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

[Javier Cerezo]

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 Javier 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!! --     “Many Smiles Begin Because Of Another Smile . . . ."   Regards, Rashi

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