AMBER: PTRAJ $ Antechamber

From: Andrew Box <>
Date: Thu, 10 Mar 2005 06:47:29 +0000

I ran ptraj as specified in the amber7 tutorial 'Generalized Born solvent
model' on a Linux server in Amber8.

The problem is that the pdb files that were generated had no charge
information, and since it is a non standard molecule amber does not have a
library file for it.

Following this i wrote a script to convert the pdb files to prepin format,
using the -c bcc option to generate the charges, then convert then back to
pdb (using -c bcc). The pdb files formed still have no charge information,
but the NEWPDB.PDB file generated does have the charge information.

So, i ask: Is PTRAJ supposed to put the charge information in the pdb file
and is antechamber able to write/generate charge information in to pdb files
with no library files.

The PTRAJ script i used is as follows:

reference bar.crd
RMS reference out bar.rmsd
trajout MD_DATA/trx.pdb PDB

The scripts used to convert the pdb files to prepin and back to pdb are as

1) Done in a 2.8 GHz P4 with Amber7 running RedHat Enterprise3.0

        antechamber -i $pdb_name -fi pdb -o $prep_name -fo prepi
        antechamber -i $prep_name -fi prepi -o $new_pdb -fo pdb


2) A 94 node, 194 CPU Linux Cluster based on Xeon 2.8 GHz cpus, running
Fedora Core 3.

        /usr/local/bin/mpiexec antechamber -i $pdb_name -fi pdb -o
$prep_name -fo prepi -c bcc
        /usr/local/bin/mpiexec antechamber -i $prep_name -fi prepi -o
$new_pdb -fo pdb -c bcc

Any advice would be very much appreciated

SEEK: Now with over 80,000 dream jobs! Click here:

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Mar 10 2005 - 06:53:00 PST
Custom Search