[gmx-users] Incorrect bond in top file
jalemkul at vt.edu
Mon Aug 27 18:09:06 CEST 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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