[gmx-users] Invalid atomtype format (Justin Lemkul

[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

-- 
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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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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