AMBER Archive (2008)

Subject: Re: AMBER: how to ger resp charge for a residue?

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Oct 31 2008 - 01:33:42 CDT

Quoting WJ Ding <dingwanjian_at_gmail.com>:

> I am trying to create the library for a non-standard residue with tleap. I
> have created atoms, residue, and unit, and set element, bond and zmatrix.
> When I checked the unit, it always said

Concerning the building of a FF library, you might be interested in
reading information about the Tripos mol2 file format:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#15
    & the use of LEaP for molecular fragments
http://q4md-forcefieldtools.org/Tutorial/leap.php

> "ERROR: The unperturbed charge of the unit: 0.190640 is not integral.
> WARNING: The unperturbed charge of the unit: 0.190640 is not zero."
> The charge for a residue should be integral, right? I calculated the resp
> charge for the whole molecular with Gaussian. I know there must be
> difference in resp charge bewteen the whole molecule and the residue. My
> point is how to
> solve this problem? How could I get resp charge for a residue (except
> R.E.D.)?

It depends what is the strategy you applied to develop your fragment
(it might not be an integer) and which type of fragment you decided to
built.
For instance:
- the charges for a central/terminal fragment for a modified
amino-acid (AA*) should be indeed an interger (for standard charge
derivation)
- the charges for a central fragment for a modified nucleotide (Nuc*)
should also be an interger (for standard charge derivation)
- the charges for a terminal fragment for a modified nucleotide (Nuc*)
should _not_ be an interger (for standard charge derivation)
- you could imagine your own strategy here (non-standard charge derivation)

You can easily check that using LEaP:
xleap -f leaprc.ff99
charge ALA => integer
charge NALA => integer
charge CALA => integer
charge DA => integer
charge DA5 => not integer
charge DA3 => not integer; but DA5 + DA3 = integer

Using R.E.D. the building all those fragments is quite simple.
You provide a P2N file generated using Ante_RED.pl:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3

Then to execute R.E.D. you add in this file the INTRA-MCC keyword to
define the intra-molecular contraint(s) you want to used to define the
central fragment of your AA*, and/or the INTER-MCC keyword to define
the inter-molecular contraint(s) you want to used to define the other
fragments (terminal AA*: 1 INTER-MCC; central/terminal NUC*: 2
INTER-MCC)

See the tutorial:
Central fragment for AA*:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
terminal fragment for AA*:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#13
other fragments for Nuc*:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14

With R.E.D.-IV, a user will be able to build all those different
fragments in a single step in a multi-molecule charge fit: modified
amino-acid + modified nucleotide + modified sugar...

regards, Francois

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