Dear Pär,
The QM/MM code assigns atomic numbers based on the first letter of the atom name and the mass. Currently it is assumed that the nitrogen mass does not exceed 15.0 u. You can modify the source code accordingly. Edit
$AMBERHOME/AmberTools/src/sqm/qmmm_module.F90
look for the code fragment
elseif( Upcase(atom_name(1:1)) .eq. 'N') then
if(atom_mass > 13.0d0 .and. atom_mass <= 15.0d0) then
atomic_number = 7 !Nitrogen
and replace 15.0d0 with a number that is large enough for your purposes and recompile.
All the best,
Andy
On Sep 7, 2012, at 8:49 AM, Hakansson P. wrote:
> Dear all,
> I better add to my question below that I am using amber 11 and
> atom type (for N2O) is defined in prmtop as
> %FLAG AMBER_ATOM_TYPE
> %FORMAT(20a4)
> n1 n1 o
>
> My question is how to change from 14N to 15N in QM/MM simulation.
> Kind regards,
> Pär
>
> Dr Par Hakansson (B30/room 3047)
> NMR group, School of Chemistry
> University of Southampton
> SO17 1BJ, UK
> Office tel.: +44(0)23 80594146
> ________________________________________
> From: Hakansson P. [P.Hakansson.soton.ac.uk]
> Sent: 06 September 2012 23:57
> To: amber.ambermd.org
> Subject: [AMBER] Unable to correctly identify element N1
>
> Dear amber community,
> I am looking to explore 15N2O in water (dynamical effects) where 15N2O is treated as QM region.
> A 14N2O classical simulation is completed and changing the mass
> to 15N is possible in this case. However, when starting up energy minimisation for
> 15N-mass in a QM/MM simulation I get:
>
> LOADING THE QUANTUM ATOMS AS GROUPS
> Mask :1; matches 3 atoms
> Unable to correctly identify element N1
>
> are there additional changes needed when introducing isotope in QM/MM simulation?
>
> Kind regards,
> Pär Håkansson
>
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--
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Mon Sep 10 2012 - 14:00:03 PDT
