[gmx-users] Reg pdb2gmx for Cyclic peptide
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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