Hello gromacs users, I am trying to use pdb2gmx to bring my crystal structure into gromacs environment. The protein in the crystal has glycosidic linkages. In charmm, I could attach these carbohydrate structures using PATCH command.
What is the equivalent of doing this in gromacs? My initial search of the gromacs manual and forums suggest I build a new residue that already incorporates this patch and add the new bonding type to the specbond.dat. However, I am looking to see if there is a more generic approach; it is likely that there I may need to attach different types of linkages, in which case, generating a new residue every time becomes tedious. Thanks, Kaushik -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
