Re: [AMBER] query

From: David Case <>
Date: Thu, 2 Jan 2020 20:13:55 +0000

On Thu, Jan 02, 2020, ankita mehta wrote:
>" can we pass a variable file name to sander during system command"
>if no , what will be the alternate?
>Screenshot is attached herewith. I want to run sander in a loop and
>everytime previous cycle restart should be the inpcrd file of next cycle.
>and my bellymask is also changing at each cycle of loop.

You don't say what happens when you execute the code you have shown.

I guessing(?) that the language here is perl. If that is correct, try
replacing the single quote symbols in the system command with double
quotes; the former may be preventing variable interpolation.

(If this is some other language, the same error could be occuring.)

Aside: It's well worth your time to learn about "here files" (Google on "here
files perl" or just "here files" for shell scripts. You don't have to
write out the mdin file line by line....

...good luck...dac

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Received on Thu Jan 02 2020 - 12:30:02 PST
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