Ok, thank you, but i don't understand if I have to minimize (optimize)
ligand structure and in what params before antechamber usage, or not?
whether a ligand conformation will have an effect on prmtop content or not?
Thank you again
2011/9/26 Brian Radak <radak004.umn.edu>
> 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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--
****
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Received on Mon Oct 03 2011 - 14:30:03 PDT
