Re: [gmx-users] Invalid atomtype format (Justin Lemkul
On 4/30/20 7:10 AM, Sadaf Rani wrote: Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:- https://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 There's a lot to go through here with multiple ligands so I'm not going to be able to go through your files line-by-line. You have duplicate bond entries somewhere. Make your system simpler. Run *only* one ligand at a time through pdb2gmx to figure out which one is triggering the problem. Also note that you should remove the extraneous number 1 from all your [ bonds ] lines in your .rtp entries. They're going to lead to incorrect format in the resulting topology. Just specify the pairs of atoms that are bonded. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Invalid atomtype format (Justin Lemkul
Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:- https://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 Thanks. Sadaf -- 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] Invalid atomtype format (Justin Lemkul)
On 4/29/20 7:41 PM, Sadaf Rani wrote: Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Remove the blank lines from the end of atomtypes.atp and it works fine. Note that you should not be including LJ parameters in atomtypes.atp. Those are for ffnonbonded.itp. The atomtypes.atp file needs only the atom type and its mass as it is only used by pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Invalid atomtype format (Justin Lemkul)
Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Thanks and Regards. Sadaf -- 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.
