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

[vivek sharma]

Hi,
Thanks Manoj and Alan for your quick response. I am already using the
ambertools to generate the topology and these topologies are
successfully accepted in gromacs. I will have a look at alternate
methodologies and workflow that you guys have suggested.

My question is can I have any idea that which version of AMBER FF
should be used in this case of drug-enzyme complex?
Also, can I have any idea about the selection of MD parameters, (which
goes in mdp file) that should be used in this case?

With thanks,
Vivek

On 21 September 2010 12:24, Alan <alanwilter at gmail.com> wrote:
> 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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>>
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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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