AMBER Archive (2003)

Subject: Re: writing mol2 files using antechamber

From: David A. Case (case_at_scripps.edu)
Date: Sat Mar 22 2003 - 12:08:29 CST

On Sun, Mar 23, 2003, Giulio Rastelli wrote:

> I would like to write a mol2 file of a protein with stbyl atom types and
> amber charges, starting from a pdb. Antechamber seems to produce mol2
> files
> with aminoacid residues all numbered 1

Antechamber is designed to work with single residues (such as ligands),
and not (yet?) with polymers. You might be able to create a script to
edit antechamber's output, but there is a fair amount of coding involved
to get exactly what you are looking for.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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