Or why not trying acpype?<div><br></div><div>Cheers,</div><div><br></div><div>Alan<br><br><div class="gmail_quote">On 9 September 2011 07:37, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 9/09/2011 4:21 PM, Yun Shi wrote:
<blockquote 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></div>
Someone needs to do some work and report back :-)<div class="im"><br>
<br>
<blockquote type="cite"><br>
GLYCAM force field assigns negative force constants to some
dihedrals, and when <a href="http://amb2gmx.pl" target="_blank">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 href="http://amb2gmx.pl" target="_blank">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 href="http://amb2gmx.pl" target="_blank">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></div>
Seems like a straightforward job for regular expression replacement
using sed/perl/python/whatever. It might even be a one-liner.<br><font color="#888888">
<br>
Mark<br>
</font></div>
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