[gmx-users] Pdb2gmx for cyclic Peptide

[Justin Lemkul]

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
>

-- 
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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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