Hi all,
I think I found the culplrit. It was not overlaps but a mess up in the vdw term of a non-standard residue, the parameters of which I imported from CHARMM. All good now, the minimization works :)
Thanks for all your help and suggestions!
—
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>
---
On 2. Jun 2023, at 16:26, Bhattacharjee, Sinjini <bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>> 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 Wed Jun 07 2023 - 06:00:02 PDT
