I think you can go for Swissviewer rather going for modeller On Sat, 17 Dec 2016 at 12:04 PM, Seera Suryanarayana <paluso...@gmail.com> wrote:
> Dear Justin, > > > > I apologize you as I am wasting your valuable time. > > > > I have peptide with 69 residues and some of the SER and THR residues > > are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 > > and 69) have been modeled by modeller . I have chosen charmm36 force > > field. > > When I executed the command > > > > pdb2gmx -f 1th1.pdb -o 1th1_processed.gro -water spce -ignh > > > > I got following error. > > > > Fatal error: > > > > Atom OXT in residues GLU 69 was not found un rtp enrty GLU with 15 > > atoms while sorting atoms. > > > > Here I am sending a link which has the coordinate file. > > > > > > > https://drive.google.com/file/d/0B5HyqLWajWjHWjMyY25Cc3lSRTA/view?usp=drive_web > > > > Kindly tell me how to solve this error. > > > > Thanks in advance > > Surya > > Graduate student > > India. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
