RE: AMBER: Calculating dipole moments

From: Ross Walker <>
Date: Wed, 28 Nov 2007 13:57:12 -0800

Hi Austin,

Which version of AMBER are you using here?

> When I use this input:
> Ligand_cap_coul trisaccharide
> &cntrl
> ntr=0,
> nstlim=20000, nscm=2000,
> ntx=5, irest=1, ntb=2, ntpr=100, tempi=300.0, ig=974651,
> ntp=1, taup=1.0,
> dt=0.0001, nrespa=1,
> ntt=1, temp0=300.0, tautp=2.0,
> ntc=2, ntf=2, tol=0.000001,
> ntwr=10000, ntwx=100,
> scnb=1.0, scee=1.0, dielc=1, cut=10.0,
> icfe=1,
> /
> &dipoles
> RES 1 4

You do not specify clambda which I would assume you need for a TI
calculation. TI should not do anything to modify the charge array from which
the permanent dipole is calculated. Hence it should not affect the dipole
result. However, I have never tested this. Are you using the same prmtop
file for the free energy and regular calculations?

Or are you using AMBER 8 in which case you have a perturbed prmtop file
which has delta charges. I'm not sure how this works since I think you
specify delta charges but the prmtop ends up with the absolute charges (or
not?) so in this case take a look in the prmtop file and see if the charges
look reasonable (scale them by 18.2223). Also note that I really have no
idea whether one could expect dipole printing to work with AMBER 8
thermodynamic integration. Amber 9 there is no reason why it shouldn't work
as far as I can tell but there may be issues (read bugs ;-). ) I'll need
more details about what you are running to look further.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Dec 02 2007 - 06:07:13 PST
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