Dear Jane,
thank you so much for sending the script. Luckily, the binding site I am
looking at is on the proteins surface, so I hope that it won't be to
difficult to use the APR method.
I am currently trying to get the apr.py script running and I am stuck
with an error message saying that it cannot find :
49.CA, which is the
atom I defined as H1 in the apr.in file.
Do you happen to also have an updated version of the apr.py script?
Kind regards,
Andreas
On 02/02/2017 09:46 PM, Jian Yin wrote:
> Dear Andreas,
>
> Thanks so much for your feedback on the APR tutorial. I've added the
> feature of recognizing residue numbers into Zalign.py. You can download the
> updated version of this script from here:
>
> https://github.com/janeyin600/Zalign
>
> 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 <andreas.tosstorff.cup.uni-muenchen.de>
> Date: Wed, Feb 1, 2017 at 5:05 AM
> Subject: [AMBER] APR - atom selection
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> 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:
>
> :LYS.CA
>
> 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
> Germany
> Tel.: +49 89 2180 77059
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Tue Feb 07 2017 - 06:00:03 PST
