[gmx-users] Re: How to apply distance restraints
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 2 10:45:36 CEST 2005
On Thu, 2005-06-02 at 09:29 +0530, Kirti Patel wrote:
> 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
> Thanks for replying.
> 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 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
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