Hello,
I added some bicarbonate ions to my protein of interest through packmol,
and have been trying to minimize it. Whether I add counterions, water, or
neither, I keep getting the same type of errors. The minimization will
start, and shortly afterwards the energy of the bicarbonate ions will get
very high until the system crashes with a segmentation fault:
NSTEP ENERGY RMS GMAX NAME NUMBER
180 -2.9907E+07 9.3976E+10 9.8870E+12 O2 6302
BOND = 695.1052 ANGLE = 5340.6089 DIHED =
5674.3885
VDWAALS = -2632.3300 EEL = -26695.4667 HBOND =
0.0000
1-4 VDW = 1293.9465 1-4 EEL = ************* RESTRAINT =
0.0000
This happens even though I am restraining the bicarbonate ions in my
minimization:
restraintmask=':MOL'
and looking at the structure, the bicarbonate ions of very high energy are
not particularly close to anything else. I thought these high energies
would come with overlapping atoms, but this doesn't appear to be the case.
What else can I try? Thanks in advance!
Best,
Christian
--
*Christian Seitz*
PhD Candidate, Biochemistry & Biophysics | UC-San Diego
NSF GRFP Fellow, Amgen Scholar
McCammon lab <https://mccammon.ucsd.edu/> and Amaro lab
<https://amarolab.ucsd.edu/>
cseitz.ucsd.edu <cseitz.elon.edu>
[image: www.linkedin.com/in/christianseitz21]
<http://www.linkedin.com/in/christianseitz21>
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Received on Thu Aug 04 2022 - 13:35:10 PDT
