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 <[email protected] <mailto:[email protected]>> 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 > -- > gmx-users mailing list [email protected] <mailto:[email protected]> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected] <mailto:[email protected]>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] <mailto:[email protected]> | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] <mailto:[email protected]> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : [email protected] <mailto:[email protected]>
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