Hi David,
Thanks a lot.
Yes.. The problem is there..the starting energy in step 0 of md is much
higher .. and nowhere near the energy in last step of minimization. How
should I look into the matter?
Yes i do have one non-standard residue.. my ligand..
Also when i visualized the structures after minimization, and what i
observed is the liagnd molecule loses its original connectivity. And the
new ligand in minimized structure is distorted and broken. Why this could
be happening?
I'll check the smaller MD run and visualize the trajectory.
On Wed, Oct 10, 2012 at 4:46 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Oct 10, 2012, Jitesh Doshi wrote:
>
> > I am running minimization in three steps, with PBC on,
> > 1. all atoms restrained
> > 2. only protein backbone atoms restrained
> > 3. all atoms free
> >
> > all with 2500 steepest descent and 5000 conjugate gradient steps.
> >
> > and then moving to run heating and equilibration with following input
>
> Make sure the energy at step 0 of the dynamics matches the last step of
> minimization. Make sure that checkoverlap (in ptraj) reports no bad
> contacts.
>
> Run a short (serial) simulation with ntpr=1, ntwx=1, nstlim=100. Visualize
> your trajectory and look for suspicious behavior.
>
> You have a big system, and this may not be easy. If there is any
> non-standard
> part of your setup (not just ordinary amino acids...) look in that region
> first.
>
> ...dac
>
>
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--
Jitesh V. Doshi
Research Associate,
Bioinformatics Centre,
University of Pune.
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Received on Wed Oct 10 2012 - 05:30:03 PDT
