Hello,
I’m still stuck at the equilibration stage. Here are the changes I’ve made
so far:
1. Adjusted restraints:
1. 5 kcal/mol·Å² on all heavy atoms (minimization, NVT, NPT)
2. 2 kcal/mol·Å² on all heavy atoms (minimization, NVT, NPT)
3. 0.5 kcal/mol·Å² on the backbone only (minimization, NVT, NPT)
4. Finally, ran without any restraints (minimization, NVT, NPT)
2. Used ntt = 3 during the NPT phase.
3. Set the time step to 1 ps.
I suspect the issue might be related to parameter generation for the
complex.
Here’s the LEaP input file I used:
source leaprc.protein.ff19SB
source leaprc.DNA.OL24
loadoff terminal_monophosphate.lib
source leaprc.water.tip3p
addAtomTypes { { "ZN" "Zn" "sp3" } { "S3" "S" "sp3" } }
loadamberparams frcmod.ions1lm_126_tip3p
loadamberprep ZAFF.prep #Load ZAFF prep file
loadamberparams ZAFF.frcmod #Load ZAFF frcmod file
complex = loadpdb /home/simulation/complex.pdb
bond complex.83.ZN complex.7.SG
bond complex.83.ZN complex.10.SG
bond complex.83.ZN complex.28.SG
bond complex.83.ZN complex.31.SG
solvatebox complex TIP3PBOX 15.0
addionsrand complex Na+ 55 Cl- 40
savepdb complex complex_solvated.pdb
saveamberparm complex complex_zaff_solvate.prmtop
complex_zaff_solvate.inpcrd
quit
I tried using another system, and I am using CPU for equilibration so there
is definitely a problem with parameter generation.
Thank You
On Fri, Oct 10, 2025 at 12:45 PM Surabhi Singh 24933024 <
surabhi_s.bt.iitr.ac.in> wrote:
> Hello,
> I am working on protein-DNA complex, and while doing equilibration I'm
> getting vlimit error...
> So, I have generated .prmtop, inpcrd from tleap (without any error just
> warnings of close contacts )
>
> Now I'm
> 1. minimizing the system( cycle 10000), then Heating (rm to 298K quickly,
> 25000) and NVT ( NPT @ 298K,) all with restrain 10 (on the solute atoms)
> 2. Again minimizing the system( cycle 10000), then Heating (rm to 298K
> quickly, 25000) and NVT ( NPT . 298K,) all with restrain 2 (on the solute
> atoms) this time
> 3. This time I'm not using restain in minimization or equilibration,
> This is the file for gradual heating and equlibration NVT)
> '''
> rm to 298K slowly,
>
> &cntrl
>
> imin = 0, ntx = 1, irest = 0,
>
> ntpr = 1000, ntwx = 1000, ntwe = 0,
>
> ntc = 2, ntf = 2, ntb = 1,
>
> nstlim = 300000, dt =0.002,
>
> nmropt = 1, ntt = 3, gamma_ln = 2.0,
>
> ntp = 0, taup = 0.2, pres0 =1.0,
>
> &end
>
> &wt type='TEMP0', istep1=0, istep2=50000, value1=10., value2=100., &end
> &wt type='TEMP0', istep1=50001, istep2=150000, value1=100., value2=100.,
> &end
> &wt type='TEMP0', istep1=150001, istep2=200000, value1=100., value2=298.,
> &end
> &wt type='TEMP0', istep1=200001, istep2=300000, value1=298., value2=298.,
> &end
> &wt type='END' &end
> '''
> I'm getting this error of vlimit exceeded
> vlimit exceeded for step 223546; vmax = 34.0225
> vlimit exceeded for step 223547; vmax = 204.7433
>
>
> PLease help me out how should I resolve this.
> Thankyou
>
>
>
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Received on Thu Oct 30 2025 - 21:00:02 PDT
