[gmx-users] Pdb2gmx for cyclic Peptide
jalemkul at vt.edu
Fri Sep 14 16:35:29 CEST 2012
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.
> 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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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