AMBER Archive (2009)

Subject: Re: [AMBER] RESP RED

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Sep 12 2009 - 09:35:16 CDT

Dear s. Bill,

> I am using R.E.D. to derive the charge of my molecule.
> My molecule composes of two fragments, I  set the total charge of my
> molecule to +1, charge of fragment 1 to -1, and charge of fragment
> 2 to +2.

Sorry, I do not understand you. In a P2N file, you set the total
charge of a whole molecule & the charge value(s) of constraint(s) for
atom(s) and/or group(s) of atoms. You do not define the total charge
for the molecular fragment you want to build. The total charge of this
fragment is correct - only if the constraint(s) used is/are correct.

> After calculating charge using RESP-C1,

  RESP-C1: HF/6-31G* CHELPG algo., 2 stage RESP fit qwt=.0005/.001

Do you have a particular reason for using theis charge model ?
So far, I think this charge model was never used:
  RESP-C1 was only created by analogy to RESP-A1.

> I found the sum of partial charges on fragment 1 not equal to -1,
> also charge on fragment 2 not equal to +2.
> Could you help me out and tell me why that happened and how I can
> achieve portioning the charge with setting the sum of charge on
> fragment 1 to -1 and on fragment2 to -2?

This is difficult to understand which fragment you want to build
without a drawing or at least more explanation about your molecular
system. You can get public help from the Amber & q4md-fft mailing
lists. R.E.D. Server provides private assistance where you can send us
more information about your project so that we can assist you in the
building of the P2N files required for the FF library you want to build.

You have many examples of fragment building @
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
  &
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php

Is there an example corresponding to what you want to do ?

> Also, which model do you prefer? RESP-A1 or RESP-2, or something else.
> I just studying binding energy of some inhibitors inside an active site.

Here, you need to think to which force field you want to use:
If your active site is a protein, you might use ff03 from Duan et al.
or ff99SB for Hornak et al.
RESP-A1 is the charge model to be used with the Hornak et al. FF; It
is available in R.E.D.-III.2. It has been renamed into RESP-A1A in
R.E.D. Server/R.E.D.-IV
RESP-A1B is only available in R.E.D. Sever/R.E.D.-IV and corresponds
to the charge model used in the Duan et al. FF.
See http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php

regards, Francois

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