[AMBER] Incompatibility of coordinate file with topology after minimization

From: Houcemeddine Othman <houcemoo.gmail.com>
Date: Sat, 20 Jun 2020 15:16:13 +0200

Dear all,
I am running a restrained minimization step of a
protein+solvent+counterions system using the following input

minimization parameters
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
Sydney Brenner Institute of molecular bioscience
University of the Witwatersrand
 The Mount, 9 Jubilee Road,
Parktown 2193, Johannesburg,
 Gauteng, South Africa.
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Received on Sat Jun 20 2020 - 06:30:03 PDT
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