[gmx-users] Energy minimization, of peptide-ligand, tearing peptide apart

Richard Kerr rakerr at umich.edu
Fri Aug 12 15:15:29 CEST 2016

Hi everyone

I am currently trying to perform a peptide-ligand (~4000 and 110 Da
respectively) simulated annealing study using gromacs (5.1.2) with Amber
force fields.  Under the initial energy minimization step (minim.mdp and
nvt.mdp) I am finding that the step fails.  It then kicks out pdb files,
which when opened depicts a ligand that has 'exploded' with the peptide
fragmented into a number of pieces.

Under the same conditions, I can get the peptide to run with a ligand about
twice the size of the above, which follows through to completion of all
annealing steps to gain output pdb files.  Accounting for a peptide only
system, the peptide will also follow through to completion.

Is anyone able to suggest how to optimize the minim/nvt files, or make
sense of the log file.

I have linked to the minim, nvt and output log files below.


Log details (md_temp.e20786725)

Any help would be greatly appreciated.


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