[gmx-users] Preparation of the pdb for MD simulation

James Starlight jmsstarlight at gmail.com
Wed Aug 1 21:51:48 CEST 2012

Dear Gromacs users!

I have pdb structure wich I'd like to prepare for my MD simulation. In
that case this structure consist of some non-standart residue (
chromophore) wich is covalently bonded to the protein's backbone. The
main problem is that this structure has some missing residues on both
of the C and N termi wich I'd like to rebuild ussing some
homology-building teqnique. Could you advise me some web server wich
could done such simple task? It's very important that I 'd kile to
prevent deletion of the my heteroatomic groups after processing of my
pdb  into that server ( e.g servers like pdb2pqr delete heteroatomic
group after processing ).

Thanks for help


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