On Fri, Jun 02, 2023, Bhattacharjee, Sinjini via AMBER wrote:
>Hi, I am trying to minimise a protein-membrane system using sander and
>pmemd in Amber20. However, the calculation keep crashing in the first cycle
>with the following error:
>
>
>NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 1.0669E+24 C19 90066
>
> BOND = 31692.7352 ANGLE = 68711.0955 DIHED = 59597.8979
> VDWAALS = NaN EEL = -12389.2862 HBOND = 0.0000
> 1-4 VDW = NaN 1-4 EEL = -149672.0786 RESTRAINT = 0.0000
>
As you can see from responses, lots of people encounter this problem. For
me, the best approach is one that has not been mentioned yet: use the
"checkstructure" action in cpptraj. Load the prmtop file, and your initial
coordinates (in a trajin line). Then "checkstructure reportfile clashes"
will put a list of bad contacts and bad bond lengths into the "clashes" file.
I find that this can help narrow down bad parts of the structure. You don't
necessarily need to fix all of them, but if you have two atoms exactly on
top of each other (distance of 0) they need to be fixed. Making sure that
all the bond lengths are at least roughly correct is also a big help in
finding problems with input PDBs or missing tleap commands.
.....dac
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Received on Fri Jun 02 2023 - 09:30:03 PDT
