[AMBER] Ligand appears broken after minimization

From: Jitesh Doshi <dosjitesh.gmail.com>
Date: Wed, 21 Nov 2012 15:19:15 +0530

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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Received on Wed Nov 21 2012 - 02:00:02 PST