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

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:-

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 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


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