Your restraint energy is 0,so I think your setup isn't right. What's your
full input file?
Also where did you get the bicarbonate parameters? The 1-4 eel is
unprintably high, so I suspect some intramolecular interaction is off.
On Wed, Jul 20, 2022, 4:53 PM Christian Seitz via AMBER <amber.ambermd.org>
wrote:
> 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 - 13:35:12 PDT
