AMBER Archive (2009)

Subject: Re: [AMBER] radical simulation

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jul 24 2009 - 05:27:34 CDT

Dear Jeffrey,

As Manish Kumar suggested you, you can use the R.E.D. tools for that.
You will have to use Ante_R.E.D. to prepare the P2N input(s) for
R.E.D. Once again, you will have to select well defined
conformation(s) here [minimum(a) or transition state structure(s)].

Ante_R.E.D. is going to re-order the atoms in your initial PDB file so
that the methyle & methylene groups will be clearly identified for
RESP charge derivation. You will have to carefully check the atom
connectivities in the p2n file to reflect the correct topology of your
radical. Provide the correct spin multiplicity & total charge in the
P2N file (if different from 1 & 0, respectively).

See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3 for the
description of the p2n file format.

See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php &
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
for examples of p2n files & charge derivation for whole molecules &
molecular fragments.

You might adapt the theory level of QM computations in the R.E.D.
source code as well (since you have a radical).

regards, Francois

> Can MD simulation be used to radical system? We are going to
> check the water distribution around a radical molecule. Are the
> atomic charges obtained as the neutral molecule for radical?
> As in the following example, should the electron pair on C4 atom be
> restraint during RESP calculation?
>
> e.g.
> REMARK
> REMARK
> ATOM 1 C1 MOL 1 -3.428 1.900 -0.002 1.00 0.00
> ATOM 2 C2 MOL 1 -2.207 1.365 0.000 1.00 0.00
> ATOM 3 N3 MOL 1 -2.383 0.036 0.001 1.00 0.00
> ATOM 4 C4 MOL 1 -3.668 -0.267 -0.001 1.00 0.00
> ATOM 5 N5 MOL 1 -4.308 0.887 -0.003 1.00 0.00
> ATOM 6 C11 MOL 1 -5.789 0.971 -0.005 1.00 0.00
> ATOM 7 C13 MOL 1 -6.191 2.459 0.008 1.00 0.00
> ATOM 8 C15 MOL 1 -1.350 -0.988 0.004 1.00 0.00
> ATOM 9 H17 MOL 1 -1.336 1.856 0.002 1.00 0.00
> ATOM 10 H19 MOL 1 -3.648 2.876 -0.003 1.00 0.00
> ATOM 11 H21 MOL 1 -6.151 0.531 -0.827 1.00 0.00
> ATOM 12 H23 MOL 1 -6.155 0.515 0.806 1.00 0.00
> ATOM 13 H25 MOL 1 -7.189 2.536 0.007 1.00 0.00
> ATOM 14 H27 MOL 1 -5.822 2.912 -0.803 1.00 0.00
> ATOM 15 H29 MOL 1 -5.825 2.897 0.830 1.00 0.00
> ATOM 16 H31 MOL 1 -1.777 -1.892 0.004 1.00 0.00
> ATOM 17 H33 MOL 1 -0.782 -0.888 0.821 1.00 0.00
> ATOM 18 H35 MOL 1 -0.780 -0.889 -0.812 1.00 0.00
> TER
>
> Many thanks.
>
> Jeffrey Yang

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