[gmx-users] Reg pdb2gmx for Cyclic peptide

vidhya sankar scvsankar_agr at yahoo.com
Thu Sep 13 17:42:19 CEST 2012

Dear Justin Thank you for your Previous reply,
                                                                           sorry for the inconvenience  to you personal Mail.

I am doing MD  Cyclic Peptide  When I run  pdb2gmx , The Conect Infromation in pdb file are ignored . so that it is not able to connect the first and last residue in cycle .  But it construct and .top and.gro files  successfully while in .gro file the end residues are closed as NH3+ and COO-(charge)  (it means there is Bond between Nitrogen and carbon atom)

It consider the N atom of first residue as NH3+    and   C atom as COO-(charge)   but I need to take N as peptide Nitrogen and C as Peptide carbon 

What Should i do  to invoke conect information when i run pdb2gmx tool
Also Can i Directly Edit  (it means removing excess hydrogen and oxygen atom by ; symbol)   .top an .gro files and can i use  to proceed further ?
Thanks in Advance 

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