Thanks for your help..... On Wed, Feb 9, 2011 at 11:44, Mark Abraham <mark.abra...@anu.edu.au> wrote:
> On 9/02/2011 4:56 PM, bipin singh wrote: > > Sir, > Actually ARG is present as a ligand bound to RNA molecule.... > > > Then you've got work to do. pdb2gmx copes well with linear polymers of > predefined monomers, which you don't have. You will need to become very > conversant with chapter 5 of the manual. Various how-tos on the wiki will > help too. > > One solution is to generate a topology for base-bound-to-arginine by hand > based on the building blocks in the respective .rtp files. Check that > topology is useful for vacuum MD of that hybrid residue. Then modify it to > be a new .rtp entry, update the forcefield database accordingly. Only then > can pdb2gmx deal with it. > > Another is to use AMBER's leap module to generate a topology for > base-bound-to-arginine, and convert the topology representation somehow > (IIRC there might be a tool for that). Then proceed as above. > > Mark > > > On Wed, Feb 9, 2011 at 11:16, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 8/02/2011 9:27 PM, bipin singh wrote: >> >>> Hi all, >>> I am getting following during while running >>> pdb2gmx for a RNA molecule....i am using amber99sb force field parameters >>> >>> The details of the error is as: >>> >>> Fatal error: >>> In the chosen force field there is no residue type for 'ARG' as a >>> starting terminus >>> For more information and tips for troubleshooting, please check the >>> GROMACS >>> website at http://www.gromacs.org/Documentation/Errors >>> >> >> Sounds like you have an arginine residue. Why? >> >> Mark >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > * > --------------------------------- > Thanks and regards > Bipin Singh > * > * > * > > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- * --------------------------------- Thanks and regards Bipin Singh * * *
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