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On 9/09/2011 4:21 PM, Yun Shi wrote:
<blockquote
cite="mid:CAHktH276VJqEfwcz0+1_W5Pmh=oqsDDnhLqgtJfiXjuD7b_eyw@mail.gmail.com"
type="cite">Hi all,<br>
<br>
I understand this problem has been discussed before, but it seems
no conclusion has been drawn.<br>
</blockquote>
<br>
Someone needs to do some work and report back :-)<br>
<br>
<blockquote
cite="mid:CAHktH276VJqEfwcz0+1_W5Pmh=oqsDDnhLqgtJfiXjuD7b_eyw@mail.gmail.com"
type="cite"><br>
GLYCAM force field assigns negative force constants to some
dihedrals, and when <a moz-do-not-send="true"
href="http://amb2gmx.pl">amb2gmx.pl</a> 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 <a
moz-do-not-send="true" href="http://amb2gmx.pl">amb2gmx.pl</a>,
that is:<br>
<br>
...........................<br>
<br>
# get all force constants for each line of a dihedral #<br>
my $lines = $i -1 +$numijkl;<br>
for(my $j=$i;$j<=$lines;$j++){<br>
my $period = abs($pn{$j});<br>
if($pk{$j}>0) {<br>
$V[$period] = 2*$pk{$j}*$cal/$idivf{$j};<br>
}<br>
<br>
...........................<br>
<br>
the "$pk{$j}>0" is modified to "$pk{$j}!=0".<br>
<br>
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 <a moz-do-not-send="true"
href="http://amb2gmx.pl">amb2gmx.pl</a> could be used to
correctly convert the topology.<br>
<br>
I am wondering if the first approach has been validated, since the
second one seems complicated and laborious to carry out.<br>
</blockquote>
<br>
Seems like a straightforward job for regular expression replacement
using sed/perl/python/whatever. It might even be a one-liner.<br>
<br>
Mark<br>
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