It seems that the clashes were not removed since the vdw energy is Nan at
the first step. Look at atom C19 and see what is near it.
On Fri, Jun 2, 2023, 10:27 AM 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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Received on Fri Jun 02 2023 - 08:00:03 PDT
