Do you want to minimize each frame of the trajectory, or the final
result? Also, will you be eliminating solvent otherwise present for
these calcs?
In any case, if a deeper minimum is desired, a cooling regime may work
better than simple minimization.
Bill
On 4/20/17 2:33 AM, Manjula Saravanan wrote:
> Dear Sir,
> I have done 50ns MD for my ligand-protein complex. I need to post
> minimize the MD trajectory in order to use it for the normal mode
> calculations. Kindly suggest me the minimization file format for post MD
> minimization. How to use it for normal mode calculations, Please help me
> out in this regard.
> I hope you will do the needful.
>
> *With Best Regards*
> *S. Manjula*
> *Research Scholar*
> *Laboratory of Biocrystallography and Computational Molecular Biology*
> *Department of Physics*
> *Periyar University*
> *Salem-11*
> *Tamilnadu*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 20 2017 - 03:00:03 PDT
