Re: [AMBER] pdb snapshots

From: Lizelle Lubbe <>
Date: Wed, 15 Nov 2017 12:16:13 +0000

Hi David,

I am using cpptraj version 15 available at our high performance computing centre

It doesn't mention any arguments not being processed. This is from the cpptraj_output:

  'md2_9_stripped_snapshot.pdb' is a PDB file (1 file per frame), writing charges to occupancy column and vdW radii to B-factor column, using PDB V3 res/atom names, Parm CDOM_CPLX_rnb_stripped_box.prmtop: Writing 3000 frames (1-Last, 15)

It reads everything except keepext and conect from the input

How can I fix this?

From: David A Case <>
Sent: 14 November 2017 03:26 PM
To: AMBER Mailing List
Subject: Re: [AMBER] pdb snapshots

On Tue, Nov 14, 2017, Lizelle Lubbe wrote:
> I used the following to create pdb snapshots of my trajectory:
> trajin
> trajout snapshot.pdb pdb offset 15 multi vdw pdbv3 conect keepext
> Unfortunately the pdb extension is not kept (files are named
> snapshot.pdb.1 etc) and the conect records are not written at the end

Which version of cpptraj are you using? (It's printed out at the top of the
output). Simplest explanation is that you are using old code.

Also, look in the cpptraj output to see if it says anything about arguments
not being processed.


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Received on Wed Nov 15 2017 - 04:30:03 PST
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