Re: [AMBER] QM-MM atoms input

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Mon, 12 Sep 2011 13:12:26 +0100

Hi Shruti,
You can/should use qmmask for specifying both residues and atoms.
It works just like other 'mask' specifications in AMBER, see e.g. Appendix C
in the AMBER 11 manual.
Example selecting only the side chains of some specific residues:
qmmask='( :78,82,207,211,215 & !.N,HN,CA,HA,C,O )'

--Marc

On 12 September 2011 12:00, Shruti Koulgi <koulgi.shruti.gmail.com> wrote:

> How do we mention the list of "QM atoms" in the input file?
> We use "*qmmask*" variable for specifying the *residues* and "*iqmatoms*"
> for specifying the atoms.
> What is the format to write the "*iqmatoms*" in the input file.
>
> _______________________________________________
> 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 Mon Sep 12 2011 - 05:30:04 PDT
Custom Search