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!!!
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Nemo me impune lacessit*
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Received on Mon Sep 26 2011 - 11:30:04 PDT
