Hi Sinjini,
your VDW and 1-4 VDW energies are NaN but the BOND ANGLE and DIHEDRAL ones
are very high, too. Are you absolutely sure that no clashes remain in your
starting structure and that you set the box sizes correctly? How did you do
that checking, would leap for example give you atom distance warnings?
Kind Regards,
Thomas
On Fri, Jun 2, 2023 at 4:27 PM Bhattacharjee, Sinjini via AMBER <
amber.ambermd.org> 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
>
>
>
> This is my initial input:
>
> Minimize
> System minimization:
> &cntrl
> imin=1, ntmin=1, nmropt=0
> maxcyc=2000, ncyc=1000,
> ntx=1, irest=0,
> ntpr=100, ntwr=100, iwrap=0,
> ntf=1, ntb=1, cut=10.0, nsnb=20,
> igb=0,
> ibelly=0, ntr=1,
> restraintmask=“.CA", restraint_wt=20.0,
> &end
> /
>
>
> I added the membrane using packmol-memgen.
> The system size is huge and I checked and removed clashes in the protein
> and the non-standard residues.
> Can you please tell me what is the problem and how can I solve this? Is it
> an issue with the parameters or the structure?
>
>
> Many thanks,
> —
> Sinjini Bhattacharjee
>
> PhD Student
> Molecular Theory and Spectroscopy
> Max-Planck-Institut für Kohlenforschung
> 45470 Mülheim an der Ruhr, Germany
>
> email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>
> ---
>
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Fri Jun 02 2023 - 08:00:05 PDT
