AMBER Archive (2004)

Subject: Re: AMBER: conversion of Amber 7 .pdb file to .bgf file

From: Peter Oelschlaeger (
Date: Thu Mar 04 2004 - 20:00:34 CST

I converted an xyz file from an MD simulation into a pdb file:
ambpdb -p parmfile <xyzfile> pdbfile
Then I get a pdb file with e.g. 2HB, 3HB instead of 1HB, 2HB.
I tried the -pqr, -aatm -bres options. -aatm only creates chunk, the
other ones give 2HB, 3HB.
Then I tried to convert the files using protonate with -b, as written in
the manual, but in our Amber7 copy option -b doesn't exist.

Thanks for the help,

On Thu, 2004-03-04 at 14:59, David A. Case wrote:
> On Thu, Mar 04, 2004, Peter Oelschlaeger wrote:
> > It seems as if Amber 7 names the
> > hydrogens in another way than pdb convention.
> ambpdb should give hydrogen names that match those in RCSB (the pdb). If
> you find different results, you should report that as a bug. Please provide
> a specific example.
> ...thanks...dave case

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