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 <[email protected]> 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110909/cce09225/attachment.html ------------------------------
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