[gmx-users] Re: How to apply distance restraint

[Kirti Patel]

Dear David,

Could you please explain me what could be the error and how to solve it, as I am new user of Gromacs.

Thanks for replying.

Kirti



Dear David,
> With "not working" I meant the distance restraints that I am applying
are not properly applied.
> The distances still remain greater than what I am applying.
That is not the same thing as not working. Increase the force constant
and check the energy file for restraint violations.

>
> The other problem is of imidazole ring of histidine which looses its
planarity, to form an envelop
> conformation.
Topology error.

>
> Thanks for replying.
>
> Kirti
>
>
> What do you mean by "not working"?
>
> On 5/31/05, Kirti Patel <kirti at chem.iitb.ac.in> wrote:
> >
> > Dear All,
> >
> > I am working with 16mer peptide with L and D chirality. I want to put
> > distance restraints for four
> > of its residues. For a poly L conformation, distance restraints are
> > properly applied but for
> > heterotactic peptide the distance restraints are not working. Can anybody
> > help me in these regard.
> >
> > Also one the histidines imidazole ring moves out of plane (gets tilted)
> during cooling in
> > simulated annealing specially if it is of D chirality. Any suggestions
> in these are most welcome.
> >
> > Thank you.
> >
> > Waiting for reply.
> >
> >
> > Kirti Patel
> > "Research Scholar"
> > Bio-organic Lab,                     Room No. c307
> > Department of Chemistry,             Hostel 12
> >                    Indian Inst. of Technology
> >                             Bombay
> > Ph. No.-022-25764780(Lab),
> >         022-25764168(Lab)
> > Fax No:-022-25767152
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


Kirti Patel
"Research Scholar"
Bio-organic Lab,                     Room No. c307
Department of Chemistry,             Hostel 12
                   Indian Inst. of Technology
                            Bombay
Ph. No.-022-25764780(Lab),
        022-25764168(Lab)
Fax No:-022-25767152