AMBER Archive (2004)

Subject: AMBER: questions for PNA parameters

From: Suwipa saen-oon (suwipa_at_atc.atccu.chula.ac.th)
Date: Fri Mar 26 2004 - 21:36:56 CST

Hello

I have been using AMBER 7.0 for some months to perform the MD
simulations on the Enzyme system which is mainly on HIV-1 Protease.
Now, I am moving to another story of the PNA-DNA duplex system in
order to support and understand the experimental results that we have
cooraperation with the organic synthesis Professor. At the moment, I
face to the difficult part of generating the parameters for the PNA
(peptide nucleic acid) chain which is not the normal PNA backbone but
it is the modified backbone of normal PNA. Therefore, I would like to
ask for any suggestion how I can generate the parameter set for this
modified-PNA chain. Which procedure you would reccomend me ? I am
thinking to use the antechamber to genarate the parameters for this
PNA chain and using AMBER FroceField for the DNA chain, How do you
think, that is sound reasonable or not ?
 
Thank you very much in advacne for all suggestions.

Best regards

Suwipa Saen-oon

Computational Chemistry Unit Cell, Chemistry Department, Faculty of
Science, Chulalonfkorn University, Bangkok, THAILAND

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