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

[Mark Abraham]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110909/2d8daa1c/attachment.html>