AMBER Archive (2009)

Subject: Re: [AMBER] Charge problem

From: Remya S R (amm07bi022_at_students.amrita.ac.in)
Date: Tue May 05 2009 - 07:19:51 CDT

Sir,
DB75 is 2,5'Bis[4-guanylphenyl]furan
Sir I generated the force-field parameters using ff.gaff

----- Original Message -----
From: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Tuesday, May 5, 2009 5:46:32 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [AMBER] Charge problem

what is DB75? how did you generate the force field parameters for it?
it can be neutral as a molecule but very unlikely for atoms to have no
partial charges.

On Tue, May 5, 2009 at 7:43 AM, Remya S R
<amm07bi022_at_students.amrita.ac.in>wrote:

> Sir,
> I tried the simulation of dna complexed with DB75. When I view
> the minimized structure of the complex in Xleap, the charge of the ligand
> appears to be zero. Is this right? Will it be possible for a ligand bound to
> DNA, to be neutral? Please help me.
>
> Sincerely
> Remya S.R
>
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