Hi,
making your own residue and running it in an MD is explained in tutorial
4b on the amber homepage. Argon is a pretty simple case, so building the
mol2 file will be straightforward. You will need non-bonded parameters for
Ar-Ar contacts though, and these Amber can not generate for you, they need
to determined beforehand (e.g. by QM calcs or fitting to experiments).
Kind Regards,
Thomas
On Tue, May 8, 2012 11:40 pm, jit mukherjee wrote:
> I want to simmulate liquid argon using amber. I have created a fcc
> lattice of argon as a starting coordinate file. but, argon is not an
> inbuild unit in AMBER. so, how can I produce an unit for argon? what
> is the format of creating a library file? Do I need to use
> antechamber?
>
> On 5/8/12, David A Case <case.biomaps.rutgers.edu> wrote:
>> On Tue, May 08, 2012, jit mukherjee wrote:
>>
>>> Ok, I connect the two units by TER. Now, how to define the non-bonded
>>> parameters between the two units XXX and YYY?
>>
>> ??? You should not need to do anything, since loading both the Amber and
>> the
>> gaff parm files gives LEaP everything it needs to know.
>>
>> The usual advice:
>> 1. don't be afraid to experiment
>> 2. Read any error messages carefully; use the search box at the amber
>> mailing
>> list archives to see if the problem has come up before.
>> 3. if you can't solve a problem and need to ask on the list, be specific
>> about what you did and exactly what error messages you received.
>>
>> ....dac
>>
>>
>> _______________________________________________
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>>
>
>
> --
> jit mukherjee
>
> _______________________________________________
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>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed May 09 2012 - 01:00:03 PDT
