[gmx-users] error while running pdb2gmx
Hello GROMACS users, I have phosphorylated Serine residue in my protein (140 residues) of interest, now when I run pdb2gmx I get this following error Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms while sorting atoms. I checked aminoacid.rtp, there is no separate entry for OXT there.When I did the simulation for the same protein prior phosphorylation I did not get this error. What is the reason for this and how should I rectify this error? Please help me with this regard Regards, Hasthi -- gmx-users mailing listgmx-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
Re: [gmx-users] error while running pdb2gmx
On 11/13/13 6:02 AM, hasthi wrote: Hello GROMACS users, I have phosphorylated Serine residue in my protein (140 residues) of interest, now when I run pdb2gmx I get this following error Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms while sorting atoms. I checked aminoacid.rtp, there is no separate entry for OXT there.When I did the simulation for the same protein prior phosphorylation I did not get this error. What is the reason for this and how should I rectify this error? Please help me with this regard Presumably you have modified the force field to include the phosphorylated residue, correct? Have you followed every one of the steps shown at http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue? If you need further help, we will need more information, which will include (at minimum): 1. Snippet of the PDB file containing the problematic residue 2. Your exact pdb2gmx command 3. The screen output of pdb2gmx (all of it, not just the error message) -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] error while running pdb2gmx
Probably the default behaviour of pdb2gmx for termini is not appropriate for your input. Use pdb2gmx -ter and choose wisely Mark On Nov 13, 2013 12:03 PM, "hasthi" wrote: > Hello GROMACS users, > I have phosphorylated Serine residue in my > protein (140 residues) of interest, now when I run pdb2gmx I get this > following error > > Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms > while sorting atoms. > > I checked aminoacid.rtp, there is no separate entry for OXT there.When I > did the simulation for the same protein prior phosphorylation I did not get > this error. What is the reason for this and how should I rectify this > error? > > Please help me with this regard > > > Regards, > Hasthi > -- > gmx-users mailing listgmx-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 listgmx-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
