Hi Alan,<br><br>I am not sure if my acpype version is not updated. But I did try, and it behaved the same as <a href="http://amb2gmx.pl">amb2gmx.pl</a> for dihedrals.<br><br>Yun<br><br><br>Or why not trying acpype?<br>
<br>
Cheers,<br>
<br>
Alan<br>
<br>
On 9 September 2011 07:37, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>
<br>
> On 9/09/2011 4:21 PM, Yun Shi wrote:<br>
><br>
> Hi all,<br>
><br>
> I understand this problem has been discussed before, but it seems no<br>
> conclusion has been drawn.<br>
><br>
><br>
> Someone needs to do some work and report back :-)<br>
><br>
><br>
><br>
> GLYCAM force field assigns negative force constants to some dihedrals, and<br>
> when <a href="http://amb2gmx.pl/" target="_blank">amb2gmx.pl</a> was used to convert prmtop file to gromacs top file, these<br>
> negative values seem to be ignored. Some people proposed that we change the<br>
> 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<br>
> negative signs, and correspondingly, change the phase shift from 0 to 180.<br>
> 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<br>
> one seems complicated and laborious to carry out.<br>
><br>
><br>
> Seems like a straightforward job for regular expression replacement using<br>
> sed/perl/python/whatever. It might even be a one-liner.<br>
><br>
> Mark<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
<br>
<br>
<br>
--<br>
Alan Wilter SOUSA da SILVA, DSc<br>
Bioinformatician, UniProt - PANDA, EMBL-EBI<br>
CB10 1SD, Hinxton, Cambridge, UK<br>
<a href="tel:%2B44%201223%2049%204588" value="+441223494588">+44 1223 49 4588</a><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110909/cce09225/attachment.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110909/cce09225/attachment.html</a><br>
<br>
------------------------------<br>
<font color="#888888"><br></font>