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 <[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] > > 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]. > > 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] | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list [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]. > 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]
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