Dear All,
I am writing in connection with a problem which I have recently faced using Amber22. Me and my colleagues are users (not superusers) on the newest supercomputer in Hungary named 'Komondor', we are using the program on this computer. I wanted to use the 'ccptraj' module for stripping solvent molecules. Using parm, parmstrip and parmwrite out commands I did not get the proper output (box_strip.prmtop) from my input (box.prmtop) however I got a message that everything went fine, the stripping is finished and no problems occured. The box_strip.prmtop does not appear in the folder I was working in, not even when I apply a direct pathway. I tried to use trajin, trajout, outparm commands unsuccesfully, nothing has changed.
Is this problem in connection with the settings of the supercomputer itself or the Amber22? I executed stripping succesfully on a daily basis with Amber16 on another supercomputer, so I find this case very unusual. Can you give me some tips about the possible sources of the problem? If the supercomputer's settings are probably not fine, I will forward your recommendations to the maintainers of Komondor with your permission.
Thank you for your help!
Sincerely,
Aliz Rimóczi
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Received on Fri Dec 01 2023 - 01:30:03 PST
