[gmx-users] Reg pdb2gmx for Cyclic peptide
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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