On Mon, Dec 09, 2024, ZHENG, siqiong [Student] via AMBER wrote:
>
>I'm repeatedly encountering an issue while trying to run tutorial B5 using
>AmberTools24 on Ubuntu 24.04. The command I used is as follows:
>
>parmchk2 -i cro.prepin -f prepi -o frcmod.cro -a Y -p $AMBERHOME/dat/leap/parm/parm10.dat
>
>After executing this command, the process stops with the following message, resulting in an empty ‘frcmod.cro’ file and an ‘ANTECHAMBER.FRCMOD’ file sized 15.4 kb. I've attached the prepin file for reference.
Odd. Here is what I see on running that command:
bethe% parmchk2 -i cro.prepin -f prepi -o frcmod.cro -a Y -p $AMBERHOME/dat/leap/parm/parm10.dat
Invalid atom name (N3) in the LOOP section.
I don't immediately see how to fix the problem, or why you are getting
different behavior than I am. (I'm using Ubuntu 22.04, which *might* be
relevant -- what does 'gcc --version' report on your machine?)
One thing to try: convert the prepin file to pdb format, and visualize it.
Does everything look like you expect it to?
I hope someone else on the list might see something that I am missing.
....dac
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Received on Mon Dec 09 2024 - 13:30:03 PST
