Dear all,
I am running a restrained minimization step of a
protein+solvent+counterions system using the following input
minimization parameters
&cntrl
imin = 1, maxcyc = 7000, ncyc = 1000, cut = 12, ntb = 1, ntr = 0, igb = 0,
drms = 0.01
/
sander -O -i energy_min1.in -o energy_min1.out -c sructure_start.rst7 -p
structure.prmtop -r structure_min1.rst7 -ref sructure_start.rst7
Everything runs successfully. However, the resulting minimized structure
(structure_min1.rst7) contains lesser information (2 Mb) than the starting
structure (sructure_start.rst7, 3Mb). It is also not compatible with the
topology file (structure.prmtop).
Do you have any idea about what might be happening here?
Thank you
--
Houcemeddine Othman
www.bioinfo-on-dunes.net
Sydney Brenner Institute of molecular bioscience
University of the Witwatersrand
The Mount, 9 Jubilee Road,
Parktown 2193, Johannesburg,
Gauteng, South Africa.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 20 2020 - 06:30:03 PDT
