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

[Yun Shi]

Hi Alan,

I am not sure if my acpype version is not updated. But I did try, and it
behaved the same as amb2gmx.pl for dihedrals.

Yun


Or why not trying acpype?

Cheers,

Alan

On 9 September 2011 07:37, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

>  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 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, 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 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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--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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