AMBER Archive (2006)

Subject: Re: AMBER: ff for drug-dna complex and drug atom types assignment

From: Barbault Florent (florent.barbault_at_paris7.jussieu.fr)
Date: Mon Oct 23 2006 - 13:37:53 CDT

Hello,

In my mind it will be more correct to use gaff (general amber force
field) for the drug and ff99 for the dna. For assigning atom types you
can do it automatically with the antechamber software.
Hope this will help you.
Best regards.
Florent

On Mon, 23 Oct 2006 19:08:59 +0300
  Kateryna Miroshnychenko <kateryna_mirosh_at_ire.kharkov.ua> wrote:
> Dear all,
>
> I want to simulate DNA-drug complex, but after reading mail archive
>I'm
> still unsure what will be the best choice for the force field: I'm
> hesitating between ff98 and ff99 or may be mix of them (98 for DNA,
>99 for
> drug). As it is written in the manual, ff98 is tuned for nucleic
>acids
> whereas ff99 is better for organic molecules. What will be your
> advice?
>
> Besides I have question about the assigning atom types for the
>carbon
> atoms in the chromophore of the drug (see attached figure). Should
> they all (except that in C=O group) have CM or CA type?
>
> Thank you in advance,
> Katya
>
>
>
>
> ********************************************
> Kateryna Miroshnychenko
> post-graduate student
> Department of Biological Physics,
> Institute of Radiophysics and Electronics,
> National Academy of Sciences of Ukraine,
> 12, Proskura st., Kharkiv, 61085, Ukraine
> E-mail:kateryna_mirosh_at_ire.kharkov.ua
> ********************************************

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