after tleap, generate the pdb structure of your system using ambpdb. Open
in any visualizer (like pymol) and then check ur ligand. Then you will
understand wha Kshatresh mean. The problem is not at minimization step. It
is before that, when you make your system using tleap.
Hirdesh
On Wed, Nov 28, 2012 at 7:04 AM, Jitesh Doshi <dosjitesh.gmail.com> wrote:
> I am sorry but I really am not understanding what do you mean by
> parameterizing ligand. I checked forcefield file, but there is nothing such
> as 'ATTN NEED Revision', what could be the problem? The bonds are getting
> broken and reformed with other atoms.
>
>
> On Wed, Nov 21, 2012 at 3:26 PM, Kshatresh Dutta Dubey
> <kshatresh.gmail.com>wrote:
>
> > probably, you have not parameterize ligand
> > correctly, recheck ligand forcefield file during antechamber run ,
> > there must be some -
> > 'ATTN NEED Revision' like statement. Put there proper values of force
> > constants.
> >
> >
> > On Wed, Nov 21, 2012 at 3:19 PM, Jitesh Doshi <dosjitesh.gmail.com>
> wrote:
> >
> > > Hi all,
> > >
> > > I am running a minimization using sander on some ligand-protein
> complex..
> > > but when I retrieve the PDB file of minimized structure, ligand appears
> > > broken as seen in attached pictures..
> > >
> > > I had used gaussian on the ligand and used the gaussian output as input
> > for
> > > antechamber..
> > >
> > > My input file is:
> > >
> > > &cntrl
> > > imin=1, maxcyc=7500, ncyc=2500,
> > > ntpr=5,ntr=1,restraint_wt=10, restraintmask=':1-356',
> > > cut=16, ntb=1,
> > > /
> > >
> > > what could be the reason? How can I rectify this?
> > >
> > > --
> > > Jitesh V. Doshi
> > > Research Associate,
> > > Bioinformatics Centre,
> > > University of Pune.
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
> >
> > --
> >
> >
> **************************************************************************************************************************
> > Kshatresh
> >
> > <http://www.researcherid.com/rid/F-3097-2012>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jitesh V. Doshi
> Research Associate,
> Bioinformatics Centre,
> University of Pune.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Nov 28 2012 - 00:30:05 PST
