Re: [AMBER] Incompatibility of coordinate file with topology after minimization

From: David A Case <>
Date: Sat, 20 Jun 2020 21:22:06 -0400

On Sat, Jun 20, 2020, Houcemeddine Othman wrote:

>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 -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).

The default format for restart files is netcdf, which will often by
smaller than a formatted form. Use the "file" command to see which
files are formatted ("ASCII") and which are not ("data").

[The ntxo variable controls the format of restart files; but we
recommend sticking with the default unless you know you have a good
reason not to.]

How did you conclude that the min1 restart file is not compatible with
the prmtop file?


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Received on Sat Jun 20 2020 - 18:30:03 PDT
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