Re: [AMBER] error

From: David A Case <>
Date: Wed, 11 Dec 2019 11:40:39 -0500

On Wed, Dec 11, 2019, MYRIAN TORRES RICO wrote:
>Exactly, I want to run pmemd using final trayectory (.mdcrd) instead
>firsts coordinates (.crd).

You can't do this (directly): trajectory files have lots of coordinates
(frames) in them, whereas a restart file has only one set of
coordinates. pmemd doesn't know how to start from a trajectory file.

Do you have a "final" restart file (created with the "-r" flag)? Might
that not be what you want here, as a starting point for the next MD

If not, do this: use cpptraj, with trajin being the trajectory file:
choose the frame you wish to use. Set trajout to write a restart file.

Then you can use the restart file you just created. It won't have any
velocities, so you will have to set ntx=1 and tempi to the initial
temperature you want.

....hope this helps....dac

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Received on Wed Dec 11 2019 - 09:00:01 PST
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