[gmx-users] Incorrect bond in top file

[Justin Lemkul]

On 8/27/12 11:41 AM, Shima Arasteh wrote:
>
>
> Dear users,
>
>
> [ Especially dear Justin ( please don't shout at me! ) ],
>

I haven't, and won't.  I keep my caps lock off ;)  Hopefully no one gets the 
impression that I have done otherwise...

>
> As I have described it many times, I defined a new residue named FVAL in aminoacids.rtp of the force field ( CHARMM36). The first step is "generating top file". When I ran the command of pdb2gmx, the top file is generated, but it contains a bond which I have not defined in the FVAL. The incorrect bond is between H-atom of valine (  this H is one of the atoms connected to the N of valine and this N is in the backbone, The N of valine is connected to C of formyl, CA and H)  and C-atom of formyl group! ( It seems that the C of formyl doesn't form a second ordered bond with O ).
>
> aminoacids.hdb and aminoacids.rtp are the files I modified.
>

Please post the relevant .rtp and .hdb entries.  There is an error somewhere, 
but we can't determine what it is without seeing these.

-Justin

-- 
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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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