Hi All,
I have a relatively large system (70 kDa) solvated using OPC water model. When solvation is done with a 10 A margin, everything runs just fine. However, when I try to add more solvent and go to 20 A, minimization fails with the below message:
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 5 2870 5814 5817
The restart file is not written even when I specify ntwr=10 and the failure is at step 110. The error message is highly strange as well, since it refers to the amide N and carbonyl O atoms of the same residue. Not sure how it's possible for them to become too close (or too far), especially when the entire protein structure is restrained.
And finally, the same starting structure behaves perfectly fine when the number of waters is lower (and the box is smaller). With the smaller box, production MD runs to 200 ns without incident.
Has anyone seen anything like this? Why are extra waters triggering these failures? I may well be missing something but this doesn't seem to make sense.
Thanks in advance!
Sasha
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Oleksandr "Sasha" Buzko
Computational Biology
ImmunityBio
9922 Jefferson Blvd
Culver City, CA 90230
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Received on Sat Mar 16 2024 - 20:00:02 PDT
