Re: [AMBER] [BULK] Re: [BULK] Re: MM-PBSA calculation error

From: Serena Vittorio <>
Date: Thu, 7 May 2020 11:26:12 +0200 (CEST)

thanks David...I followed your suggestion and it worked out!

----- Messaggio originale -----
Da: "David A Case" <>
A: "AMBER" <>
Inviato: Mercoledì, 6 maggio 2020 18:32:42
Oggetto: [BULK] Re: [AMBER] [BULK] Re: MM-PBSA calculation error

On Wed, May 06, 2020, Serena Vittorio wrote:
>This is the result I obtained:

You are trying to give a netcdf formatted trajectory file to a program
(make_crd_hg) that expects a formatted file.

Beyond this, I'm out of my depth here, since I've never used this
workflow. For a while the default trajectory file format has been
netcdf, but it used to be formatted.

You could try using cpptraj to convert your netcdf file to the formatted
mdcrd format. That might help things out. But others on the list
probably know more than I do about the best thing to do here.


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Serena Vittorio
Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali
Università degli Studi di Messina
Viale Annunziata, 98168, Messina, Italy
Phone: +39 090 6766465
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Received on Thu May 07 2020 - 02:30:03 PDT
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