On 9/14/12 9:56 AM, vidhya sankar wrote:
Dear Justin Thanks Again for your reply
When I run Pdb2gmx using -ter
option for my Cyclic peptide and i have selected None for both termini as you
instruct in the previous mail i have got error as follows
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper
terminal entry.
How to resolve these error
Try adding the -missing flag. This is about the only situation I can think of
where this is sensible.
-Justin
For you remembrance i have pasted the previous mail Discussion
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.( Your Ansewr)
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
(Your Answer)
directives. Re-run pdb2gmx instead.
Thanks in Advance
With Regards
S.vidhyasankar
--
========================================
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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