Re: [AMBER] Imaging and connectivity error

From: Jason Swails <>
Date: Thu, 13 Aug 2015 10:06:29 -0400

On Thu, 2015-08-13 at 16:57 +0530, Harmeet Kaur wrote:
> Dear Amber Users
> My system is a receptor of 2 subunits bound with 8mer peptide, simulated
> for 1micro-sec using iwrap=1. I've used various combinations of 'image' and
> 'unwrap' to center the molecule, but the sub-units tend to diffuse out. My
> last attempt was using 'autoimage origin'. Although the molecule is now
> centered, it shows some connectivity issues (a snapshot attached for
> reference). Can I proceed with it for further analyses? If not, please
> suggest how to troubleshoot the same.

If this is really what your structure looks like (i.e., you're not
accidentally loading the wrong type of trajectory file in VMD), then no,
you can't proceed with further analyses.

Are you perhaps loading 1kcs-autoimage_dry.mdcrd as Amber coordinates
with box (by accident)?

> The script used was:
> trajin prod_1kcs.mdcrd
> strip :WAT
> strip :Na+
> strip :Cl-

These can all be combined into a single command (and should be, since
it's faster and cleaner):

strip :WAT,Na+,Cl-

> autoimage origin
> trajout 1kcs-autoimage_dry.mdcrd nobox

I highly recommend that you switch to using exclusively NetCDF
trajectories instead of ASCII trajectories. They store coordinates in
higher precision, they are much smaller on disk, they are much faster to
read into VMD and cpptraj, and they are much faster to write by sander
and pmemd. They also separate all of their data, so VMD doesn't have to
be told whether or not box information is available -- it just does the
right thing.

You can change your last trajout command to


to write a NetCDF file. Then load it directly into VMD as a NetCDF


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Aug 13 2015 - 07:30:03 PDT
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