Re: [AMBER] [q4md-fft] how to keep atom restrained in R.E.D?

From: FyD <>
Date: Wed, 07 Mar 2012 10:01:44 +0100

Dear Albert,

> I've got a ligand in protein crystal structure and I am trying to
> calculate the partial charge by R.E.D coupled with GAUSSION. However, I
> found that the atom in the ligand shift a lot and the conformation of
> the ligand is very different from that in crystal structure. I am
> wondering how to restrain the atom position when we use R.E.D coupled
> with GAUSSION?

You could use:
- geometrical constraint(s) during geometry optimization.
- if your ligand is a big molecule, you could split this molecule into
elementary building blocks; this often solves the conformation issues
you report...

Concerning geometrical constraint(s), you could follow two approaches:

-1 You generate the .com & p2n files using Ante_R.E.D.; modify the
.com Gaussian input to add geometrical constraint(s) (the ModRedundant
mode; see Once you got
the wanted optimized geometry you rename the .log Gaussian output file
into Mol_red1.log and use R.E.D. III.x or R.E.D. Server/R.E.D. IV in
mode 2 associated with the Mol_red1.p2n file.
see ; see Mode 2 page 3

-2 You add directly the geometrical constraint(s) in the P2N file;
this has been introduced in R.E.D. III.5x and R.E.D. IV, and you use
R.E.D. III. 5x or R.E.D. Server/R.E.D. IV in mode 1.
However, here the format we developed is in agreement with Gaussian
98, Gaussian 03, and Gaussian 09 up to B.01; i.e. the format we
developed has to be modified for Gaussian 09 C.01, which is currently
interfaced by R.E.D. Server. On our 'To Do' list...

-> Now which type of constraint(s) you could use?
I would use a (i) minimum of constraint(s) and (ii) dihedral
constraint(s) might be the best bet... See for instance project in
"dihedral constraints were used in the geometry optimization step to
avoid intra-molecular hydrogen bonds and transition state type
structures: HO3'-O3'-C3'-C4' = 180 deg., HO2'-O2'-C2'-C3' = 290 deg."

regards, Francois

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Received on Wed Mar 07 2012 - 03:00:02 PST
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