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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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
**************************************************************************************************************************
Kshatresh
<http://www.researcherid.com/rid/F-3097-2012>
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Received on Wed Nov 21 2012 - 02:00:03 PST
