AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Oct 31 2008 - 02:59:31 CDT

Hi Francois:
May I ask if the project of deriving RESP charges with NWChem is going
on? We NWChem users hope it is going on. Could you take advantage from
the NWChem built in method to derive ESP and RESP charges? I used it
successfully some time ago, but then get discouraged by the complex
procedure of putting that to use with Amber.

Could you also envisage that RESP charges for unusual ligands that do
not covalently bind to macromolecules could be used for docking
programs?

Thanks
francesco pietra

On Fri, Oct 31, 2008 at 7:33 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
> 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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