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.
> >
> > _______________________________________________
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> >
> >
>
>
> --
>
> **************************************************************************************************************************
> Kshatresh
>
> <http://www.researcherid.com/rid/F-3097-2012>
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>
--
Jitesh V. Doshi
Research Associate,
Bioinformatics Centre,
University of Pune.
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Received on Tue Nov 27 2012 - 22:30:02 PST
