Re: [AMBER] Single Point Energy: sander x python sander

From: Alan <>
Date: Fri, 14 Jan 2022 11:31:07 +0000

I've been using Conda ambertools 21.11.

I'm already using a small system (NALA-ALA-CALA) and, to Ray, in my first
email I gave all the steps for anyone to reproduce the issue, so yes, I'm
absolutely sure I'm using the same files.

With sander I do use ntmin=2 (steep descent) and maxcyc=0 so I want the
energies at step 0 of my systems.

I did suspect that python was doing 1 or more md steps so I played with md
in mdin for sander (igb=6, imin=0, maxcyc=0, ntmin=2, nstlim=X), where I
increased X one by one but I didn't reproduce the energies seen from

Also, it's not SHAKE since pysander inp.ntc = inp.ntf = 1 which are the
same as default in sander.

So, I dive into the code.

I'm using gitpod from

Installed `sudo apt install gfortran` there.

Then did:

./configure --no-rism --no-netcdf --no-boost

make clean && make install

Alas, it failed to build with:

[MSANDER] FC extra_pts.F90
[MSANDER] FC ../rism/amber_rism_interface.F90

   16 | use safemem
      | 1
Fatal Error: Cannot open module file β€˜safemem.mod’ for reading at (1): No
such file or directory
compilation terminated.
make[2]: *** [Makefile:172: amber_rism_interface.API.o] Error 1
make[1]: *** [Makefile:10: serial] Error 2
make[1]: Leaving directory '/workspace/msander/src'
make: *** [Makefile:4: install] Error 2
gitpod /workspace/msander $

My reasoning here was to build and compare all the original tools from
source and in a clean, fresh, isolated machine.

On Thu, 13 Jan 2022 at 17:37, David A Case <> wrote:

> On Thu, Jan 13, 2022, Alan wrote:
> >In details:
> > Python x Sander
> >error angle : 0.48950 % 4.29874 x 4.27770
> >error bond : 2.04820 % 0.75717 x 0.77300
> If your bond and angle energies don't agree, then debugging should be much
> easier.
> Check things like doing a single-step minimiation instead of MD. But it
> probably comes down to getting into the code and seeing what the python
> gb_input is doing (in complete detail); I don't know that off the top of my
> head. It's possible that the python interface is doing somthing like
> setting SHAKE by default, which you are not doing in your sander
> calculation.
> You might try a very small system to see if that helps find the
> differences.
> ...dac
> _______________________________________________
> AMBER mailing list

Alan Silva πŸš²πŸŠβ€β™‚πŸƒβ€β™‚πŸ‡§πŸ‡·πŸ‡«πŸ‡·πŸ‡¬πŸ‡§
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Received on Fri Jan 14 2022 - 04:00:02 PST
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