AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM simulation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Sep 03 2009 - 15:43:45 CDT

Hi Gaurav,

You specify qmmask='.....' in the qmmm namelist. Take a look at the
documentation for specifying masks. Page 254 of the AMBER 10 manual. Chances
are you want to use the : specifier. E.g. ':251' to specify residue 251 to
be QM.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of gaurav panwar
> Sent: Thursday, September 03, 2009 1:12 PM
> To: amber_at_ambermd.org
> Subject: [AMBER] QM/MM simulation
>
> I want to do QM/MM simulation of my docked protein but i am not sure
> how to
> specify docked ligand atoms in input files for QM calculations. Please
> send
> me suitable informations.
>
> --
>
> Gaurav Panwar
> M.S.(Pharm)
> Center for Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research
> Mohali
> Contact no: 9914519541
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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