Re: [AMBER] Issue in drug parameter

From: David A Case <>
Date: Sun, 1 Mar 2020 08:32:04 -0500

On Sat, Feb 29, 2020, SHAUNAK BADANI wrote:
>I am a beginner and I am trying to generate drug parameters for
>my system. I followed the antechamber tutorial and was able to
>generate drug.lib and drug.frcmod files (attached). When I run a short
>equilibration of the drug in vacuum, it seems to be fine but when I use
>these parameters to run a short drug+water system equilibration, the
>system seems to break apart (drug+water.png image attached). Can anyone
>help me in figuring out why this is happening?

Looks like an imaging issue: use the autoimage command in cpptraj to
pack everything back into a primary unit cell, then see if things look
better. (Note that imaging or lack of imaging has no effect on the
actual simulation; it only affects visualization.)

...good luck...dac

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Received on Sun Mar 01 2020 - 06:00:04 PST
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