[AMBER] running QM/MM calculations

From: David A Case <david.case.rutgers.edu>
Date: Wed, 29 Jul 2020 07:40:51 -0400

On Wed, Jul 29, 2020, 辛志宏 wrote:

>I refer a method from a reference " The reactant state was taken from
>the previously minimized structure, upon deletion of all water molecules
>beyond a shell of 5A around the enzyme-substrate complex",
>so, I saved the last frame as QM/MM input file, and then recreat inpcrd
>and prmtop file due to the quantity of total molecular changed.

OK...but now you have a non-periodic system (since you've removed most of the
waters). So it won't work to just put back in the box information. If you
want to follow exactly what was done in the reference you chose, you'll have
to read what they did after deleting all those water molecules.

[Note that Amber users generally would have no need to strip away all those
water molecules if the intent was to continue with QM/MM calculations. Are
you sure the authors weren't just doing pure QM or something after stripping
the distant waters?]

> Small interatomic distances encountered:
> 54 49 4.54D-01
> Atoms too close.

This can't be debugged remotely: you will have to look at atoms 49 and 54 and
try to figure out what is going on. (From your report, I can't even tell what
program you are running....)

>In addtion,I got more than 500 rst file when I saved the rst file by the
>following script, how to only save the rst file of the last frame from
>the mdcrd file?
>Create an input file, “ptraj.in”:
>trajin DLFae4-MFA_equil.mdcrd

Use the "lastframe" option to trajin. Type "help trajin" at the cpptraj
prompt to get lots of useful information.


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Received on Wed Jul 29 2020 - 05:00:02 PDT
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