please tell us exactly what you did. this is not clear. what steps,
what rograms. did you follow a tutorial?
On 5/5/09, Remya S R <amm07bi022.students.amrita.ac.in> wrote:
> 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.gmail.com>
> To: "AMBER Mailing List" <amber.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.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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--
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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Received on Wed May 20 2009 - 14:42:59 PDT
