AMBER Archive (2009)

Subject: Re: [AMBER] radical simulation

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Sun Jul 26 2009 - 07:28:39 CDT

Many thanks for all suggestions. I will try with R.E.D.
 
  

---
Jeffrey

--- 09年7月24日，周五, FyD <fyd_at_q4md-forcefieldtools.org> 写道：

发件人: FyD <fyd_at_q4md-forcefieldtools.org>
主题: Re: [AMBER] radical simulation
收件人: "amber" <amber_at_ambermd.org>
抄送: q4md-fft_at_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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      ___________________________________________________________ 
  好玩贺卡等你发，邮箱贺卡全新上线！ 
http://card.mail.cn.yahoo.com/
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber