Re: [gmx-users] Atom OXT in residue was not found
Dear Justin, Thanks very much for your suggestion, it works well now. All the best, Qinghua On 08/09/2017 01:28 PM, Justin Lemkul wrote: On 8/9/17 7:21 AM, Qinghua Liao wrote: Hello, I want to simulate a protein with a ligand (small molecule, 15 atoms). But I have problem of generating the topology file. I added the topology of the ligand as a new residue in force field database (aminoacid.rtp), but I got the error when I run pdb2gmx interactively with -ter and chose none for the ligand: Atom OXT in residue DH2 495 was not found in rtp entry DH2 with 15 atoms The problem is that there isn't any atom named OXT in the ligand. I also searched the mailing list, someone mentioned that pdb2gmx might rename the atom name of the atoms in the ligand. I don't understand why pdb2gmx complains something like this when the atom is not in the ligand. Any suggestions? Thanks a lot! pdb2gmx is trying to apply C-terminal protein patching to your ligand. If you have listed DH2 in residuetypes.dat as Protein, don't. Also note that atom names are translated via xlateat.dat so if you have one of those atom names, and DH2 is considered a protein residue, you need to choose a different atom name. -Justin -- 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.
Re: [gmx-users] Atom OXT in residue was not found
On 8/9/17 7:21 AM, Qinghua Liao wrote: Hello, I want to simulate a protein with a ligand (small molecule, 15 atoms). But I have problem of generating the topology file. I added the topology of the ligand as a new residue in force field database (aminoacid.rtp), but I got the error when I run pdb2gmx interactively with -ter and chose none for the ligand: Atom OXT in residue DH2 495 was not found in rtp entry DH2 with 15 atoms The problem is that there isn't any atom named OXT in the ligand. I also searched the mailing list, someone mentioned that pdb2gmx might rename the atom name of the atoms in the ligand. I don't understand why pdb2gmx complains something like this when the atom is not in the ligand. Any suggestions? Thanks a lot! pdb2gmx is trying to apply C-terminal protein patching to your ligand. If you have listed DH2 in residuetypes.dat as Protein, don't. Also note that atom names are translated via xlateat.dat so if you have one of those atom names, and DH2 is considered a protein residue, you need to choose a different atom name. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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.
[gmx-users] Atom OXT in residue was not found
Hello, I want to simulate a protein with a ligand (small molecule, 15 atoms). But I have problem of generating the topology file. I added the topology of the ligand as a new residue in force field database (aminoacid.rtp), but I got the error when I run pdb2gmx interactively with -ter and chose none for the ligand: Atom OXT in residue DH2 495 was not found in rtp entry DH2 with 15 atoms The problem is that there isn't any atom named OXT in the ligand. I also searched the mailing list, someone mentioned that pdb2gmx might rename the atom name of the atoms in the ligand. I don't understand why pdb2gmx complains something like this when the atom is not in the ligand. Any suggestions? Thanks a lot! All the best, Qinghua -- 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.
