Re: [AMBER] generating methane parameters

From: David A Case <>
Date: Fri, 26 Jun 2020 08:04:06 -0400

On Fri, Jun 26, 2020, angad sharma wrote:

>i want to generate parameters for methane, but i am facing some problem

It looks like your problem has nothing to do with methane, but rather
with the flags you are using for sander/pmemd (which you don't show), or
in the "heating" step:

> Unit 9 Error on OPEN: heat.rst

First, when things aren't working, don't run a complex script that does
many pmemd runs all together; run things one step at a time, and examine
the output of each step before starting the next one.

Here, certainly you need to examine the mdout files to look for
problems. Try short, serial, runs, say with nstlim=10 and ntpr=1.
Find the simplest things you can that work, and gradually increase the
complexity of what you are doing.

...good luck...dac

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Received on Fri Jun 26 2020 - 05:30:03 PDT
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