It sounds like you would be well served by the AMBER tutorials. Here a few
suggestions, although I suspect other users with more experience may offer
different ones:
http://ambermd.org/tutorials/basic/tutorial1/
http://ambermd.org/tutorials/basic/tutorial4b/
Regards,
Brian
On Mon, Sep 26, 2011 at 2:22 PM, Алексей Раевский <rayevsky85.gmail.com>wrote:
> Hi, I'm really new user of amber. I have to build a topology, using
> ambertools 1.5, for several new residues: aminoacyladenylate (residue
> connected through carbonyl O of aminoacid to PO3-5' of adenyne) and
> aminoacyl-trna (residue connected by carbonyl O of aminoacid with 3'OH
> group
> of ribose in adenyne nucletide). I have a few questions about:
> 1. I have to add all hydrogenes with any program, but what I have to do
> with
> amynocayl-trna? The PO3 end of adenyne must be connected to the next
> nucleotide, (one free valence of P) I have to leave this place empty or I
> have to add H there?
> 2. Have I minimize or optimize the structures before using ambertool with
> any chemprogs?
> 3. What about atom types? which program I can use for structure building
> (marvinsketch, hyperchem) to avoid any problems with antechamber?
> 4. What about net charge? how can I calculate it and assign it to
> aminoacyl-trna (end' adenyne with aminoacid)?
> 5. Thank you very much!!!
>
>
> --
> ****
> *
>
> Nemo me impune lacessit*
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Mon Sep 26 2011 - 12:00:03 PDT
