AMBER Archive (2009)

Subject: Re: [AMBER] R.E.D. help please

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Jul 15 2009 - 11:35:57 CDT

Dear Bill,

> I need really a help. I am a new user in AMBER and i got completely
> confused in generating a non-standard residue charge.
> According to R.E.D. the charge is changing by changing the molecular
> orientation,

We talk here about the molecular orientation of the optimized
geometry/structure. You could do your own tests using a small molecule
by studying different orientations in MEP computation & looking at the
impact on the charge values.

> so I should define in R.E.D. which orientation I used in generating
> the charge, as well as, I can specify more than one orientation
> (and this is recommended by R.E.D.).

This is up to you: You could keep the orientation generated by the QM
program (QMRA approach) or use the rigid body re-orientation algorithm
implement in R.E.D. (RBRA approach).

> So, now, I am using Gaussian in calculation charge (pop=Mk). How
> can I specify the orientation during calculating the molecule's
> charge? Gaussian uses an internal algorithm for molecular
> orientation.

Please, read http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
In particular:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3 section -7-

> Also, should I recalculate the molecule's charge by using Gaussian
> for different orientations?

You provide the information about the reorientation approach you
selected in the P2N input file, and that's it, R.E.D. does the job.

> and in this case, how can I emerge the different Gaussian outputs
> for different orientation?

R.E.D. does the job automatically.

> or I calculate it once, and then specify different orientation in
> R.E.D.? and according to which principle, atoms used in specify
> orientation are chosen? i.e. which three atoms can I use for
> orientation specification?
> PLEASE, any one direct me and answer these simple questions?

For an answer to this question see the end of the message @
http://lists.q4md-forcefieldtools.org/wws/arc/q4md-fft/2009-07/msg00027.html

regards, Francois

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