On 12/01/12 17:19, Tyler Luchko wrote:
> On 2012-01-12, at 10:27 AM, Meli Massimiliano wrote:
>
>> Hi all,
>>
>> i would to know how i can create other solvent model, for different
>> molecule,
>> like the one contained in the directory :
>>
>> $AMBERHOME/dat/rism1d/model
>>
>> can i extract the model information from the topology (prmtop) file ?
>
> Hi Max,
>
> Unfortunately, there is no easy to use tool to do this. You can look at the prepdat.pl script in the model directory for an idea how to do this. This extracts the information from the prmtop file to create the MDL file. It is not the cleanest script but you may be able to modify if for your needs.
>
> If you look at the contents of the MDL files, it is fairly straightforward and there is a description in the AmberTools manual. You should be able to construct them by hand for small molecules, which is all rism1d can reliably handle. As has been noted on the list here before, there is one poorly name section, LJSIGMA, that is really R_min/2.
>
> Hope this helps,
>
> Tyler
>
> ________________________________________________________________
> Tyler Luchko
> Postdoctoral Associate
> Case Group
> BioMaPS Institute
> Rutgers University
> Piscataway, New Jersey
> tluchko.rutgers.edu
> 848-445-5239
>
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Dear Tyler,
thanks a lot, this was very useful.
I successfully wrote the mdl file for my molecule.
max
--
Dr. Massimiliano Meli, Ph.D
Istituto di Chimica del Riconoscimento Molecolare, CNR
Via Mario Bianco 9,
20131 Milano (Italy)
Tel: ++39-02-28500037
Tel: ++39-02-28500023
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web: http://colombo-biocomputing.org/
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Received on Thu Jan 12 2012 - 10:00:03 PST
