[gmx-users] MD on docked complex using AMBER FF

[Alan]

Also, have a read at acpype.googlecode.com.

Alan

On 21 September 2010 06:36, manoj singh <mks.amber at gmail.com> wrote:

> First, you have to develop parameter for your molecule withing Amber. Then
> you have to create .prmtop and .inpcrd files for your molecule, and than you
> can convert the Amber topology to Gromacs topology. You will need AmberTools
> and a script called amb2gmx.pl.
>
> Following links would be helpful for you
>
> http://ambermd.org/#AmberTools
>
> http://ambermd.org/antechamber/efz.html
>
> ffamber.cnsm.csulb.edu/*amb2gmx*.*pl*
>
>
> On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma <viveksharma.iitb at gmail.com
> > wrote:
>
>> Hi There,
>> I am trying to run molecular dynamics on a drug-enzyme complex using
>> amber force field. I have done it earlier using gromos FF using
>> drug-enzyme tutorial, I dont know if the parameter set (.mdp file)
>> will be same or different while using AMBER FF.
>> Any insight/comments into the matter may be of help if somebody has
>> tried using AMBER FF for docked complex in GROMACS.
>>
>> Thanks in advance.
>>
>> regards,
>> Vivek
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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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