On 9/09/2011 4:21 PM, Yun Shi wrote:
Hi all,
I understand this problem has been discussed before, but it seems no
conclusion has been drawn.
Someone needs to do some work and report back :-)
GLYCAM force field assigns negative force constants to some dihedrals,
and when amb2gmx.pl <http://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
<http://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 <http://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.
Seems like a straightforward job for regular expression replacement
using sed/perl/python/whatever. It might even be a one-liner.
Mark
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