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
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 07 2011 - 00:30:05 PDT
