your vdw energies are off scale, and the bond energies are also very high
(the water will not have bond energies, so this indicates something in the
solute has gone wrong).
in my experience, nearly every problem people report with instability for a
complex ends up being related to the ligand parameters. I suggest running
the same simulation with just your protein in water and see if you get the
same problem or not. If not, then carefully examine how you obtained your
inhibitor force field. If you do have troubles, check your relaxation
protocol and the source of the initial coordinates.
On Tue, Jun 10, 2025 at 9:29 AM Sudipti Priyadarsinee via AMBER <
amber.ambermd.org> wrote:
> Hi experts,
> I have given production runs in CUDA for an enzyme-inhibitor system in the
> OPC water model. However, I obtained the following error after a few steps
> due to a sudden increase in temperature or some other reason:
>
>
>
>
>
>
> *NSTEP = 7900000 TIME(PS) = 8800.000 TEMP(K) =********* PRESS =
> 0.0 Etot = ************** EKtot = ************** EPtot =
> ************** BOND = 45640928.0483 ANGLE = 401600.0594 DIHED
> = 2120.2028 UB = 0.0000 IMP = 0.0000 CMAP
> = 241.5422 1-4 NB = 0.0000 1-4 EEL = 0.0001
> VDWAALS = ************** EELEC = -83478.2065 EHBOND =
> 0.0000 RESTRAINT = 0.0000*
>
> A similar error is also observed in the TIP4P-ew water model for the same
> system.
> Enzyme-inhibitor system is ribonuclease A with a dinucleotide
> I have used ff19SB forcefield for protein and gaff2 for inhibitor.
> Below is my input file for your reference:
>
> Production
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> nstlim=10000000,
> dt=0.001
> temp0=300.00,
> ntpr=5000,
> ntwx=5000,
> cut=10.0,
> ntb=1,
> ntp=0,
> ntt=3,
> gamma_ln=2.0,
> ig=-1,
> iwrap=1
> /
>
> Please give me your suggestions on this.
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>
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Received on Tue Jun 10 2025 - 07:30:02 PDT
