(unknown charset) [AMBER] Antechamber preparartion

From: (unknown charset) Алексей Раевский <rayevsky85.gmail.com>
Date: Mon, 29 Oct 2012 13:57:10 +0200

Hi, my name is Alex and I want to clarify several moments I had noted
during Antechamber procedure.

Q1. How to prepare a correct molecule of the inhibitor?
Adding all hydrogenes - it is OK thanks to chemaxon and openbabel.

Q2. But what about the inital conformation (is it important or I can use
plane structure?) and atom type assignation (for example in PO3 group I
have to use O.co2 atom type, as it is mentioned in tripos mol2 manual or
http://www.ccdc.cam.ac.uk/support/documentation/gold/5_1/gold/gold.1.68.html#245104
)?

Q3. Does it make reliable convertion from pdb ro mol2 or it is better to
make some changes by hands in mol2 and then import it?

Q4. What degree of accuracy this soft can provide? And, especially, what
about biological molecule (derivatives) like ATP, modified amino acids?
As I know swissparam.ch developed for charmm27 had some problem with it.

Q5. As I'm working with amber forcefield bith in gromacs4.5.5 and amber11
I'm using AM1 bcc flag. So what about the string, is it correct?


antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc -s 2



Thank you very much!

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Received on Mon Oct 29 2012 - 05:00:03 PDT
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