[gmx-users] Fw: Did GROMACS earlier version change?

Justin Lemkul jalemkul at vt.edu
Wed Oct 10 02:18:43 CEST 2018

On 10/9/18 4:53 AM, Dr. Seema Mishra wrote:
> What happened to GROMACS? We had done lots of simulations with ATP bound protein with gromacs 4.6.3 and  GROMOS96 43a1 forcefield. Now with the same pdb file and same version, we are getting error:
> Program pdb2gmx, VERSION 4.6.3
> Source code file: /home/dr-seema/Desktop/gromacs-4.6.3/src/kernel/pdb2gmx.c, line: 727
> Fatal error:
> Atom PG in residue ATP 801 was not found in rtp entry ATP with 36 atoms
> while sorting atoms.
> HELP!!
> Tried changing PG to P as seen in gromos43a1.atomtypes file for ATP, nothing works....
> And if we have to modify files to match atoms, why do we have to do it when it was working very nicely earlier with multiple simulations?

Sounds like a classic example of not documenting what you did, and then 
having problems when you try to reproduce something.

Look at the .rtp file and you'll see that GROMOS uses weird atom names 
that all start with "A" - these names violate PDB standard (because 
several are 5 characters long) so you (or someone else) probably 
modified an .rtp file to simply strip off those leading "A" characters 
and you made it work.

As an aside (and this goes for a lot of people), please don't spam the 
list hoping to get my attention, and please don't then follow up with 
personal emails hoping to get me to reply to your question faster. I'm 
unbelievably busy, and I can no longer be the "immediate GROMACS answer 
guy" that I may have once been. I enjoy helping this community, but I 
have very little time for it these days. I give of the time that I have, 
but can't afford much more than that.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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