From: A. Bakheit <abujazz76.gmail.com>
Date: Thu, 25 Mar 2021 13:15:11 +0300

I run MMPBSA.py with the trajectories of the protein drugs complex. When I
use a short trajectory, I get a following error;

Beginning GB calculations with /home/abakheit/amber20_src/bin/sander
  calculating complex contribution...
  File "/home/abakheit/amber20_src/bin/MMPBSA.py", line 100, in <module>
line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
line 157, in run
CalcError: /home/abakheit/amber20_src/bin/sander failed with prmtop
Exiting. All files have been retained.
can only one to help me because this work I need it as comments for my
please help me.
 Ahmed Hassan Bakheit

---------- Forwarded message ---------
From: Cruzeiro, Vinicius <vcruzeiro.ucsd.edu>
Date: Wed, 24 Mar 2021, 20:12
Subject: Re: [AMBER] CpHMD with structurally different protonation states?
To: amber.ambermd.org <amber.ambermd.org>

Hello Anselm,

Unfortunately, changing anything besides the atomic charges upon a
successful protonation state change would require modifications in Amber's
source code.

All the best,

Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
San Diego Supercomputer Center
Department of Chemistry and Biochemistry
University of California, San Diego
Voice: +1(858)246-5584
From: Dr. Anselm Horn <anselm.horn.fau.de>
Sent: Wednesday, March 24, 2021 4:58 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] CpHMD with structurally different protonation states?

Dear all,

a question to the CpHMD experts:

Is it possible to apply the constant-pH simulation approach to systems,
where the protonated state differs from the deprotonated one in the
local structure, i.e. atom types and local parameters in addition to
atomic charges?

A collegue of mine was interested in investigating such a species, where
deprotonation results in a different local structure, going from
all-planar to out-of-plane distorsion.

As far as I understood the CpHMD approach implemented in Amber, the
different protonation states are realized by applying different charge
sets and Hydrogen radii to the titratable residue, keeping the
perturbation of the system small. And thus, no further change besides
atomic charges and the presence or absence of H atoms could be taken
into account.

Is this correct? Or are there some advanced options, e.g. to switch
between complete topology files?

Best regards


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Received on Thu Mar 25 2021 - 03:30:02 PDT
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