Benji,
you can achieve a simple single point energy calculation in Amber via a
structure minimization with 0 steps.
An input file (single-point.inp) for systems not too large and without a
solvent box could look like (cf Amber24 manual, chapter 21):
# Single point energy (in vacuo)
&cntrl
imin = 1,
maxcyc = 0,
ncyc = 0,
igb = 6,
&end
If you are unfamiliar with the keywords and their meaning, please have a
look into the Amber manual for their explanation to ensure that this is
the type of calculation you are interested in.
Assuming your topology and coordinate files (system.top, system.crd) are
present in the same directory, you can invoke sander via (cf. Amber24
manual, section 21.2) the following command or something similar, the
invocation is essentially the same for all types of calculation:
# Within PBS or shell script
SANDER=sander
base=system
$SANDER -O -i single-point.inp \
-p ${base}.top \
-c ${base}_min.crd \
-o ${base}_min.out \
-r ${base}_min.rst \
-inf ${base}_min.inf
The single point energy is printed in the inf file below ENERGY.
However, whether a simple single point energy on an input structure is
really suitable, depends on your research question. Note, that an input
structure has most probably deviations from the next local energy
minimum on the Amber energy hypersurface and thus is under strain,
unless relaxed (i.e. energy minimized).
Maybe this helps.
Good luck
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 24.01.2025 um 00:11 schrieb Benjamin Shugaev via AMBER:
> Hello,
> I want to run a single point energy calculation using the force fields within amber24.
> I would really appreciate if you could send me an example of an spe.in file and the commands for running the SPE.
> I am working on a PBS server and i need to generate a submit file, i could use your examples to do so.
> Currently i have a system pdb file that i ran through tleap so i have the coordinates and topology files needed.
> Thank you very much as always,
> Benji
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Received on Fri Jan 24 2025 - 01:00:02 PST
