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

[David]

On Thu, 2005-06-02 at 21:12 +0530, Kirti Patel wrote:
> Dear David,
> 
> Could you please explain me what could be the error and how to solve it, as I am new user of Gromacs.
check distance restraint section in the manual (ch. 4). if you are a new
user you should check out the nmr sections in the tutorial.

if your histidine is not planar it could be because of the dist. res.
if the topology is generated by pdb2gmx it should be ok.


> 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
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