[gmx-users] amb2gmx.pl to convert GLYCAM topology

[Yun Shi]

Hi all,

I understand this problem has been discussed before, but it seems no
conclusion has been drawn.

GLYCAM force field assigns negative force constants to some dihedrals, and
when amb2gmx.pl was used to convert prmtop file to gromacs top file, these
negative values seem to be ignored. Some people proposed that we change the
code in amb2gmx.pl, that is:

...........................

  # get all force constants for each line of a dihedral #
  my $lines = $i -1 +$numijkl;
  for(my $j=$i;$j<=$lines;$j++){
    my $period = abs($pn{$j});
    if($pk{$j}>0) {
      $V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
    }

...........................

the "$pk{$j}>0" is modified to "$pk{$j}!=0".

Others suggest to modify the original prmtop file, that is, to remove the
negative signs, and correspondingly, change the phase shift from 0 to 180.
Then amb2gmx.pl could be used to correctly convert the topology.

I am wondering if the first approach has been validated, since the second
one seems complicated and laborious to carry out.

Thanks for any advice,

Yun
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