Re: [AMBER] Simulation of complex

From: <>
Date: Mon, 19 Apr 2010 11:42:43 -0400 (EDT)


please give us a little more detail on what you actually did, instead of
what you were trying to do. Many things can go wrong in setting up a
simulation that come from e.g. naming mismatches. Please provide a list of
the commands you used, along with the results and error messages this

Working through Amber tutorials B4 and A1 may also help you here...

Kind Regards,


> Asfa Ali wrote:
>> Hi,
>> I am having a docked complex (from Autodock) of a ligand and DNA. The
>> docked
>> file is not recognised by amber, although I am using antechamber to
>> create
>> the mol2 and frcmod file of the ligand separately.
>> Is there any problem with Autodock? Can anyone tell me how to use docked
>> file from Autodock for simulation in amber?
>> I have checked the Amber mailing list but I didn't get any suitable
>> results.
>> Kindly help.
>> Asfa.
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>> AMBER mailing list
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Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Mon Apr 19 2010 - 09:00:03 PDT
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