[gmx-users] Chromophore residue patch in gromacs

[bharat gupta]

No. I am not trying to crosslink the chromophore with nay residue but I
have linked it with neighboring  Valine(68) and Leucine(64) by specifying
the bonds in specbond.dat file.

On Thu, Jan 19, 2012 at 12:09 PM, Peter C. Lai <pcl at uab.edu> wrote:

> Are you crosslinking the chromophore to an atom in residue 51?
>
> Can you generate a correct topology without the chromophore as a check?
>
> On 2012-01-19 11:50:37AM +0900, bharat gupta wrote:
> > Hi,
> >
> > I have been trying to attach the chromophore of GFP in charmm ff
> parameter
> > files. The parameters have been obtained from a published article. After
> > making the changes as per the documentation (
> >
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> )
> > , I am getting following error :-
> >
> > Atom CG is used in an interaction of type atom in the topology
> > database, but an atom of that name was not found in residue
> > number 51
> >
> > The chromophore residue number is 66, I don't understand why there is an
> > error for residue 51 . Please help me in rectifying this error ..
> >
> > Regards
> >
> > --
> > Bharat
>
> > --
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> ==================================================================
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
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