Re: [AMBER] APR - atom selection

From: Jian Yin <>
Date: Thu, 2 Feb 2017 12:46:22 -0800

Dear Andreas,

Thanks so much for your feedback on the APR tutorial. I've added the
feature of recognizing residue numbers into You can download the
updated version of this script from here:

Please let me know if there are any other problems. An alternative is to
use molecular visualization program such as Chimera to align your system.

When you use the APR scripts provided along with the AMBER tutorial, please
note that the current version of APR scripts is only a demonstration of how
to use the pulling approach to compute binding thermodynamics. It is now
applicable to most host-guest model systems. However, the application of
APR on protein systems is still under development.

So, if you are planning on computing the binding affinities for proteins
using APR, please be aware that careful adjustments of the protocols and
scripts are needed, based on the requirements of every particular system.
In addition, be extremely cautious about using the APR approach to compute
binding affinities for proteins with buried binding sites, as those may
present convergence issues due to the significant conformational change of
the protein during the pulling process.

Feel free to contact us if you need any other help with using APR.

Best Regards,

Jane Yin

---------- Forwarded message ----------
From: Andreas Tosstorff <>
Date: Wed, Feb 1, 2017 at 5:05 AM
Subject: [AMBER] APR - atom selection
To: AMBER Mailing List <>

Hi all,

I am trying to run APR on my protein. I am not sure on how to select the
atoms for zalign though. From what I can tell you have to specify the
residue and atom in this way:


My question is how to select one specifc LYS (e.g. LYS102) in case there
are several in the protein.

I tried :102.CA and :LYS102.CA but it did not work.

Any suggestions?

M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Tel.: +49 89 2180 77059
AMBER mailing list
Dr. Jane Yin
Postdoctoral Researcher
3117 Gilson Lab Office
Skaggs School of Pharmacy and
Pharmaceutical Sciences, UCSD
9500 Gilman Dr., La Jolla, CA 92093-0736
AMBER mailing list
Received on Thu Feb 02 2017 - 13:00:03 PST
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