Re: [AMBER] Trouble Creating a pdb File

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Thu, 29 Apr 2021 06:40:35 +0000

As the RST file is a binary file (NetCDF, ncrst) file, the suggested command for ambpdb may not work as intended.

A quick search revealed this issue being adress in an earlier discussion:

    The file redirect '<' only works with ASCII restarts - if this is a
    NetCDF restart use the '-c' flag instead:

    $AMBERHOME/bin/ambpdb -p cram.prmtop -c min_qmmm.rst > min_qmmm.rst.pdb

So for you files this would mean:

    ambpdb -p wat.prmtop -c wat_md.rst > pdbfile.pdb

Producing a PDB file.


Best regards
// Gustaf

On 28 Apr 2021, at 23:14, Khong, Megan <MEGAN.KHONG.UCDENVER.EDU<mailto:MEGAN.KHONG.UCDENVER.EDU>> wrote:

Hello, I am trying to create a pdb file using wat_md.rst as the input file. I am using AMBER 18. I have tried the command

ambpdb -p wat.prmtop < wat_md.rst

and I have been getting an error that says, "Error: could not read restart atoms/time". Has anyone encounter this problem before? Does anyone have any suggestions on how I can check the validity of my file?

Thank you.

-Megan Khong
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Received on Thu Apr 29 2021 - 00:00:02 PDT
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