[AMBER] "unknown flag: filename.top" error with PMEMD and topology file from CHARMM-GUI

From: Chris Lee <chrishankyu.lee.mail.utoronto.ca>
Date: Tue, 23 Nov 2021 01:25:27 +0000


In an effort to use the CHARMM36m force field for my simulations, I downloaded the AMBER topology and coordinate files from the CHARMM-GUI webserver (as .parm7 and .rst7 file extension formats).
However, when I run my job script I get the "unknown flag: filename.parm7" error.

I originally thought maybe pmemd didn't recognize the extension .parm7 and changed the extension to .top, but the error remains.

For reference, I do have working AMBER topology files for my other projects, and the general format seems the same as the topology file I downloaded from CHARMM-GUI (at least to me).

Anyone have any ideas what the problem might be? I can provide the topology file in question if anyone wants to inspect it.

Thank you,
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Received on Mon Nov 22 2021 - 17:30:02 PST
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