[gmx-users] Reg pdb2gmx for Cyclic peptide

Justin Lemkul jalemkul at vt.edu
Thu Sep 13 17:57:30 CEST 2012

On 9/13/12 11:42 AM, vidhya sankar wrote:
> 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

Use the -ter option and choose "None" for both termini.

> 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 ?

No.  This will cause errors in the [moleculetype] numbering and all successive 
directives.  Re-run pdb2gmx instead.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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