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Joined: Apr 2017
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Hi all,
I have a strange issue: when I try to equilibrate my structure, it generates this warning:
***** LEVEL -5 WARNING FROM *****
***** Undefined ANGLE style
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5
ABNORMAL TERMINATION
MOST SEVERE WARNING WAS AT LEVEL -5
The warning occurs at different times when I rerun the equilibration (30 minutes, 1 hour, 25...). I'm not able to find this warning in documentation; does anyone know what might be causing this? If you need more details, I could supply them.
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Joined: Sep 2003
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Which version of CHARMM?
Are you using any modified RTF or PARAM files?
Rick Venable
computational chemist
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I'm using charmm 40b1
These are the rtf and param files I'm using. Nothing in them is modified, however.
top_all36_prot.rtf
par_all36_prot.prm
top_all36_na.rtf
par_all36_na.prm
fmc-allpar-05302008.par
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It's a DOMDEC bug that was fixed a in later release; IIRC it mostly occurred for simulation systems with some empty space, or else systems with lots of one or two atom particles (no ANGLE terms).
I note that the file fmc-allpar-05302008.par is not part of the standard distribution.
Rick Venable
computational chemist
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What would you recommend I do? Should I just install the later version, or is there any way to avoid the bug?
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Update.
You are lucky, very lucky, that Rick did recognize the issue, given the relatively scarce information you provided.
Warning and error messages are usually not described in the documentation. This is because they are easy to find in the source code (grep is your friend!), which is about as accurate as it gets.
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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I seemed to recall finding a fix for the problem, but it looks like I'd never submitted it anywhere. I just submitted the fix to a source repository, and posted the details here
Rick Venable
computational chemist
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Hey sorry for not replying in a long time. A postdoc I work with figured out the problem a couple months back. It turns out the box size wasn't large enough, so my protein which had a large negative charge was electrostatically interacting with its image (periodic boundary conditions). This was causing holes in the box, so I increased the box size and... problem solved.
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