AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM input file error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Dec 03 2009 - 11:36:47 CST

Hi Mahesh,

> I am working on protein molecular to which i docked my ligand. I want
> to do
> QM/MM calculations on this docked molecule.
> I wants residue number 7,38,45,210 to be studied by QM. so i give
> qmmask
> line in this way as given in tutorial but it is not working properly.
> *
> qmmask=':7,38,45,210' *
> but in output file , it shows matches 2101 atoms which is not correct.
> total
> number of atoms for 7,38,45,210 residue is 87.

What are the stars doing here? Are you putting these in the input file?

Your file should look as follows:

Title
 &cntrl
  ...,
  ...,
  ifqnt=1,
 /
 &qmmm
  qmmask=':7,38,45,210',
 /

Note, however, that it is not recommended to just specify residues for the
QM region (unless it is a ligand) since this will cut the backbone and place
link atoms across peptide bonds which is a BAD idea. I would suggest looking
at the region you want to be QM very carefully and select reasonable bonds
to cut. Ideally unpolarized, true single bonds. Then work our which atom
numbers the QM atoms are (you can use something like VMD to do this, be
aware it counts from 0 and not 1 so add 1 to each number). You can also use
ptraj or ambpdb to write a pdb file from your prmtop / inpcrd which will
have the prmtop atom numbers.

Note, if you add writepdb=1 to the qmmm namelist you will get a (very crude)
pdb file written to the same directory as you run the calculation which
contains the QM region. You can load this into a visualization program and
see if you got what you expected. It will also include the link atoms so you
can see if they were placed on reasonable bond cuts.

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber