[gmx-users] Chromophore residue patch in gromacs

[Mark Abraham]

On 19/01/2012 3:17 PM, bharat gupta wrote:
> 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.

You still have to go and look at residue 51 and see what is going on. 
The problem can be independent of the chromophore, as Peter was suggesting.

Mark

>
> On Thu, Jan 19, 2012 at 12:09 PM, Peter C. Lai <pcl at uab.edu 
> <mailto: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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>     --
>     ==================================================================
>     Peter C. Lai                    | University of Alabama-Birmingham
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> -- 
> Bharat
> Ph.D. Candidate
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