AMBER Archive (2007)

Subject: RE: AMBER: Calculating dipole moments

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Nov 29 2007 - 10:08:50 CST

Hi Austin,

> the "CHARGE" and "PERT_CHARGE" sections, I get the charges for the
> unperturbed and perturbed residues, respectively. Seems
> likely that the
> charges employed in the dipole moment calculations are the from the
> PERT_CHARGE section ie using perturbed charges for the residue I am
> mutating, and unperturbed charges for the rest of the
> trisaccharide. In
> this case, what will be the best way to proceed? Extract
> structures from
> the TI calculation, generate a new unperturbed prmtop file, and then
> compute the average dipole moment for each structure?

If you are happy with scripting I believe this will be the fastest way to
go. You could write a script to take each structure in the mdcrd file - have
ptraj make a restart / inpcrd file then use this with the regular prmtop
file to run sander set to 1 step of MD and calculate the dipoles and then
use grep to extract the data you need and append it to a results file.

Anything beyond this will require modification to the code and Amber 8 is
not really maintained anymore - especially for TI calculations since the
implementation of this has change significantly in Amber 9. Do you have
access to Amber 9? If so then you could try this, I suspect that the dipoles
printing will have more chance of working correctly in Amber 9 since it uses
regular prmtop files instead of perturbed ones - hence the main charge array
(used by the dipole printing routine) should contain the real charges from
the prmtop file.

Good luck
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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