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
