Hi Astrid,
Thanks for the advice. The problem in amb2gmx.pl has not been fixed, which
still do not recognize negative pK. So what you were saying is to change
something like:
E 53: -2.500 0.00 2.0 :3.H2N :3.N2 :3.C2N :3.O2N
(45,44,46,47)
to
E 53: 2.500 180.00 2.0 :3.H2N :3.N2 :3.C2N :3.O2N
(45,44,46,47)
?
And then use amb2gmx.pl to convert?
I also wonder if it's OK to change the ">" to "!=" as in
...........................
# 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};
}
...........................
Regards,
Yun
On Wed, Sep 7, 2011 at 12:14 AM, Astrid Maaß <
astrid.maass.scai.fraunhofer.de> wrote:
> Hi Yun,
>
>
> as per amber file format specifications, the minus indicates that the
> dihedral potential of this particular set of atoms is composed of more than
> one cosine term; this appears to be properly recognized, I had not troubles
> with amb2gmx.pl in this context.
>
> The numbers in columns 6 - 11 of the gromacs-topology are the
> Ryckaert-Bellemans-constants you get AFTER converting the amber-topology to
> the gromacs. Do not worry about the signs in the GROMACS-topology.
>
> What you should check with rdparm, if you create a topology file for input
> in amb2gmx.pl with tleap/xleap/sleap anyways, whether dihedrals with
> negative force constants are present in the AMBER-topology file. The rdparm
> output is easier to read than the topology file itself and tells you, which
> torsion exactly i.e. which atoms are involved and thus which pattern of
> atomtypes is concerned (you can check the link between an atom's name and
> type in prep or mol2 files).
>
> If you find suspect torsions/force constants in the rdparm-output (or the
> FF-input.dat itself), create a copy of the FF-input.dat and modify within
> this copy the respective force constants & phase shifts for the identified
> patterns. Then create with the modified FF-input.dat a new set of top- and
> crd-files for conversion with amb2gmx.pl. As I said before, I am not sure
> whether the problem might have been fixed since the time when I encountered
> it, so check, whether the whole fuss is necessary and if the old and the new
> gromacs-topologies are indeed different.
>
> Good luck!
>
> Astrid
>
>
>
>
>
>
>
> ----- Ursprüngliche Mail -----
> Von: "Yun Shi" <yunshi09.gmail.com>
> An: "AMBER Mailing List" <amber.ambermd.org>
> Gesendet: Dienstag, 6. September 2011 20:22:06
> Betreff: Re: [AMBER] how to fill in missing parameters in tleap?
>
> Hi Astrid,
>
> I saw something like:
>
> [ dihedrals ]
> ;i j k l func C0 ... C5
> 19 18 20 21 3 0.75312 2.25936 0.00000
> -3.01248 0.00000 0.00000 ;
> 41 1 18 19 3 0.20920 0.62760 0.00000
> -0.83680 0.00000 0.00000 ;
>
> after converting glycam ff-parametized saccharide to gromacs topology
> format. I referred to gromacs manual, and knew that '3' in the fifth column
> indicates the Ryckaert-Bellemans-potential you mentioned. But could you
> tell
> me what those numbers in columns 6 to 11 mean? Which is force constant and
> which is phase shift?
>
> Thanks,
>
> Yun
>
>
> On Tue, Sep 6, 2011 at 8:21 AM, Yun Shi <yunshi09.gmail.com> wrote:
>
> > Hi Astrid,
> >
> > Thank you for the info.
> >
> > But in addition to negative force constant, there are also some negative
> > multiplicity for GLYCAM dihedral parameters. So would these negative
> > multiplicities be a problem for amb2gmx as well?
> >
> > Thanks,
> >
> > Yun
> >
> >
> >
> > On Tue, Sep 6, 2011 at 2:07 AM, Astrid Maaß <
> > astrid.maass.scai.fraunhofer.de> wrote:
> >
> >> Hi Yun Shi,
> >>
> >>
> >> I used amb2gmx.pl some time ago and if I remember correctly, for
> >> torsions, amb2gmx.pl converts the Amber-cosine series in a
> >> Ryckaert-Bellemans-potential. This was OK in most of the cases, but when
> >> amb2gmx.pl encounters a negative force constant it may not translate
> the
> >> potential correctly. I do not know, whether this behavior has been fixed
> in
> >> the meantime, but you could bypass it by using a phase shift of 180
> instead
> >> of a negative sign in the force constant for the respective term. You
> might
> >> use rdparm to check whether this difficulty would apply to your system
> >> anyways.
> >>
> >> Hope that helps
> >> Astrid
> >>
> >>
> >>
> >>
> >> ----- Ursprüngliche Mail -----
> >> Von: "Yun Shi" <yunshi09.gmail.com>
> >> An: "AMBER Mailing List" <amber.ambermd.org>
> >> Gesendet: Dienstag, 6. September 2011 01:22:19
> >> Betreff: Re: [AMBER] how to fill in missing parameters in tleap?
> >>
> >> Hi all,
> >>
> >> For this specific molecule, I wonder if it's possible to manually set
> >> parameters for the non-standard parts.
> >>
> >> I was thinking about using GLYCAM and amber99SB, while avoiding the use
> of
> >> GAFF force field, with the help of amb2gmx.pl and GROMACS software.
> >>
> >> 1. Set geometrical parameters and atomic charges to all standard
> residues
> >> using GLYCAM and 99SB.
> >>
> >> 2. Derive RESP charges for the modified TRP and thio-glycosidic linkage.
> >>
> >> 3. With GROMACS topology files, set geometrical parameters for the
> >> modified
> >> TRP and thio-glycosidic linkage according to 99SB. That is, define atom
> >> types, bonds (CT-S), angles (CT-S-CT, CT-CT-S), and dihedrals (X-CT-S-X)
> >> with corresponding parameters from 99SB. And for N, H, CA, CB, and
> indole
> >> parts of the modified TRP, just use whatever geometrical parameters from
> >> the
> >> standard TRP in 99SB.
> >>
> >> 4. Combine all these parts in GROMACS format.
> >>
> >>
> >> On Sun, Aug 28, 2011 at 6:12 AM, case <case.biomaps.rutgers.edu> wrote:
> >>
> >> > On Fri, Aug 26, 2011, Jason Swails wrote:
> >> > >
> >> > > Use parmchk. If you run the program with no arguments, it tells you
> >> how
> >> > to
> >> > > use it. By default, it will search gaff.dat and pull out reasonable
> >> > > parameters, dumping them to an frcmod file. If there's anything it
> >> > simply
> >> > > *can't* find, it will put a placeholder (all parameters are 0) and
> say
> >> > > "ATTN, need revision". You have to fix those parameters.
> >> >
> >> > Parmchk does a bit more than just look in gaff.dat: it estimates
> missing
> >> > parameters by several algorithms. In its default mode, parameters in
> >> > gaff.dat
> >> > are not put into the frcmod file; parameters it estimates on its own
> are
> >> > output; finally, things it can't figure out get placeholders.
> >> > >
> >> > > However, I would warn you that gaff dihedrals should not necessarily
> >> be
> >> > > accepted. Run short simulations to make sure they make sense, as
> you
> >> may
> >> > > have to modify some of them by hand.
> >> >
> >> > This is excellent advice.
> >> >
> >> > ...dac
> >> >
> >> >
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> >> >
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> >
> >
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Received on Thu Sep 08 2011 - 14:00:05 PDT
