Hi Boopathi, Adding hydrogen atoms to the hdb is explained in the sectio 5.6.4 of gromacs manual 4.5.4. Please refer the manual.
Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Jan 10, 2013 at 11:32 AM, Subramaniam Boopathi < boopathi...@gmail.com> wrote: > Dear All > > > I have created the pdb file for interaction of protein > with new molecules. I am able to rum the pdb file successfully but I am > facing error in the Equillibration process. The Error shows that > > > *atom HAQ is missing in residue NIC > 8 in the pdb file You might need to add atom HAQ to the hydrogen database > of building block NIC in the file aminoacids.hdb (see the manual) > * > likewise 14 atoms H atoms are missing in residu*e.Can > anyone help me how to add atom in .htp file for new molecules interacting > with protein.Thanks in advance. > > > > with regards > Boopathi.s > * > -- > 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 > -- 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