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.