AMBER Archive (2009)

Subject: Re: [AMBER] radical simulation

From: Manish Kumar (kumarmanish.amb_at_gmail.com)
Date: Fri Jul 24 2009 - 02:48:01 CDT

As long as you can correctly fit the charges, it should work. I think it is
more a problem of correct charge fitting.I would say try R.E.D for the
charge fitting. That will give you more flexibility during the charge
fitting procedure.

2009/7/24 Jeffrey <jeffry20072008_at_yahoo.cn>

> Dear all,
>
> 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
>
> -----------
> Dalian Institute of Chemical Physics,
> Chinese Academy of Sciences
> Dalian, China
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber