Hi Yun,
----- Ursprüngliche Mail -----
> Von: "Yun Shi" <yunshi09.gmail.com>
> An: "AMBER Mailing List" <amber.ambermd.org>
> Gesendet: Donnerstag, 8. September 2011 22:50:55
> Betreff: Re: [AMBER] how to fill in missing parameters in tleap?
>
> 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?
>
yes, this is exactly, what I meant.
> 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
>
Adressing the problem by fixing the code is certainly better, but since I am not much of a programming person, I am not sure, whether the fix you suggest below remedies the problem. If you decide to try both variants (modified input FF + old code; old FF + modified code), I think the resulting gromacs topologies should finally display consistent RB-coefficients.
I would appreciate if you could share the outcome of this with us.
Regards,
Astrid
>
> 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
> > >> >
> > >> >
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >> _______________________________________________
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> > >>
> > >> _______________________________________________
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> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
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Received on Thu Sep 08 2011 - 23:30:04 PDT
