Re: [AMBER] .crd error

From: David A Case <>
Date: Mon, 3 Feb 2020 08:24:22 -0500

On Mon, Feb 03, 2020, MYRIAN TORRES RICO wrote:
>I have problem with my coordenates extension. I want to launch a short
>molecular dynamic with restrictions using the final coordenates, to
>correct the distorsions in my complexe.
>At first this error appeared:
>Could not read second line of ./leap/smp-198mdk0rig_vcon3.mdcrd

I'm guessing(?) that you are trying to use a trajectory file instead of a
restart file to restart your calculation.

In Amber, the extensions don't "mean" anything (except for some places
where cpptraj tries to figure out the file format based on the
extension.) And different people use different (personal) conventions
for naming files.

The default name for a trajectory file is "mdcrd", so many people (does
this include you?) use .mdcrd as an extension for these files.
>trajin smp-198mdk0rig_vcon3.mdcrd
>trajout smp-198mdk0rig_vcon3.crd

If you look at the output of this script (which probably just copied
trajin to trajout), cpptraj will tell you what sort of file trajin is.
See if it says it is a trajectory file. If so, you will need to use a
restart file instead.

...good luck...dac

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Received on Mon Feb 03 2020 - 05:30:03 PST
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