[AMBER] EM in vacuum

From: Dmitry Suplatov <genesup.gmail.com>
Date: Tue, 2 Aug 2016 23:52:17 +0300


I am trying to run an energy minimization in vacuum of my protein (400
amino acids). The intention is to hopefully rebuild some hydrogen bonds in
a particular loop. The orientation of some backbone atoms in this loop
seems to be suboptimal, in a sense that they look like they could form
H-bonds but the angles are not very good. As a result the loop collapses
even after a short MD.

So, my question. Below is my parameter file for performing EM in vacuum.
The problem is - the atoms hardly move at all !!! The output coordinates
are almost the same as the output ones. This does not feel right.
Please suggest corrections.

Thankyou for your time.

Step-1: Minimize in vacuum only the water and ions, restraining the heavy
atoms of protein and ligands at constant 3 kcal/mol-A^2
imin=1, ! Flag to run minimization - Single point energy calculation
irest=0, ! Flag to restart a simulation - Do not restart the
simulation; instead, run as a new simulation
ntx=1, ! Option to read the initial coordinates, velocities and box
size from the inpcrd file - Coordinates, but no velocities, will be read

ntmin=1, ! For ncyc cycles the steepest descent method is used then
conjugate gradient is switched on
maxcyc=5000, ! Maximum number of minimization cycles to allow
ncyc=2500, ! The method of minimization will be switched from SD to CG
after ncyc cycles
cut=12, ! The nonbonded cutoff, in Angstroms
nsnb=20, ! Frequency at which the non-bonded list is updated
ntb=0, ! Do not impose periodic boundaries at constant volume
ntp=0, ! Flag for constant pressure dynamics - No pressure scaling
ntc=1, ! Flag for SHAKE to perform bond length constraints - SHAKE
is not performed
ntf=1, ! Force evaluation - complete interaction is calculated
igb=6, ! No continuum solvent model is used
ntxo=2, ! Format of the final coordinates, velocities, and box size
written to the restart file - NetCDF file
ioutfm=1, ! The format of coordinate and velocity trajectory files -
Binary NetCDF trajectory
ntpr=10, ! Print the progress of the minimization to output file every
ntpr steps
nmropt = 0, ! No nmr-type analysis will be done.
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Received on Tue Aug 02 2016 - 14:00:03 PDT
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