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

Dallas Warren dallas.warren at monash.edu
Wed Oct 10 02:15:16 CEST 2018

What has changed between when you performed it previously as now?
Running on a different machine?  New installation?  New coordinate
files?  What happens if you take the starting files from previous
simulations, and run those?  Have you run the linux 'diff' command on
the pdb files to see if there is actually any change?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 9 Oct 2018 at 19:53, Dr. Seema Mishra <seema_uoh at yahoo.com> 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?
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