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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Received on Tue Sep 06 2011 - 11:30:02 PDT
