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

Dr. Seema Mishra seema_uoh at yahoo.com
Tue Oct 9 10:53:31 CEST 2018


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.


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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