Many thanks for all suggestions. I will try with R.E.D.
---
Jeffrey
--- 09年7月24日，周五, FyD <fyd.q4md-forcefieldtools.org> 写道：
发件人: FyD <fyd.q4md-forcefieldtools.org>
主题: Re: [AMBER] radical simulation
收件人: "amber" <amber.ambermd.org>
抄送: q4md-fft.q4md-forcefieldtools.org
日期: 2009年7月24日,周五,下午6:27
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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Received on Sun Jul 26 2009 - 10:08:41 PDT
