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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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