Hi Jana,
.. I would suggest to use hydrogen-bond fix (HBfix) to support H-bonding between RNA base pairs.
You can apply either general HBfix (gHBfix) or ’structure-specific’ HBfix (sHBfix), where you modify just specific interactions (e.g., interactions between terminal residues). gHBfix restrains can be prepared by our gHBfix code available in the Supporting Information of Frohlking et al., JCTC 2022 paper (
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.2c00200). The output can be printed as AMBER restrains or as PLUMED input file (in case you want use Gromacs code; see help notes). In case of sHBfix (you want to modify just interaction between terminal base pairs), you can filter those interactions or prepare the input manually.
Good luck,
Vojtech.
On 14. 5. 2025, at 1:16 PM, Abhisek Jana via AMBER <amber.ambermd.org> wrote:
Hello,
I am currently performing molecular dynamics simulations of a siRNA-protein complex using the OL3-ff19SB force field combination with the TIP3P water model. The 21-mer siRNA sequence used in the study is as follows:
_AAUAUCUCGUUCUUGUGACAA_
_UUAUAGAGCAAGAACACUGUU_
While analysing the trajectory from the production run, I observed that the Watson-Crick base pairing remains stable only up to the 17th base pair. Beyond this point (i.e., after the 17-mer), the base pairing is not maintained consistently, and the hydrogen bonds between the corresponding bases are frequently disrupted throughout the simulation. I have attached the input files from all stages of the MD simulation for your reference. I would appreciate any insights or suggestions you might have regarding this instability issue. Thank you.
Step1:Minimize water and ions
&cntrl
imin=1, maxcyc=20000, ncyc=15000,
cut=10.0,
ntb=1,
ntr=1,
restraint_wt=10.0,
restraintmask='!:WAT & !:Na+ & !:Cl-',
/
Step2:Unrestrained minimization
imin=1, maxcyc=30000, ncyc=25000,
cut=10.0,
ntb=1,
ntr=0,
/
Step-3:Relax water
LET WATER MOVE
&cntrl
timlim = 999999., nmropt = 0, imin = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 500, ntwx = 500, ntwv = 0, ntwe = 0,
ntwr = 500,
ntf = 2, ntb = 2,
cut = 10.0, nsnb = 20,
nstlim = 50000, nscm = 2500, iwrap = 1,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 200.0, tautp=0.5,
ntt = 1,
ntp =1 , taup = 1.0,
ntc = 2, tol = 0.00001,
ibelly=0, ntr=1,
restraintmask=':1-873' , restraint_wt=10.0,
&end
/
Step-4:heat NPT 0.5 ns
Heating System
&cntrl
imin=0, nmropt=1,
ntx=1, irest=0,
ntpr=500, ntwr=500, ntwx=500, iwrap=1,
ntf=2, ntb=1, cut=10.0, nsnb=20,
igb=0,
ibelly=0, ntr=1,
nstlim=250000, nscm=500, dt=0.002,
ntt=1, temp0=300.0, tempi=0.0, tautp=0.5
ntc=2,restraintmask=':1-873',
restraint_wt=100,
&end
&wt type='REST', istep1=0, istep2=0, value1=1.0, value2=1.0, &end
&wt type='TEMP0', istep1=0, istep2=250000, value1=0.0, value2=300, &end
&wt type='END' &end
/
Step-5:Density Equilibration
&cntrl
imin=0, nstlim=250000, dt=0.002,
irest=1, ntx=5,
ntc=2, ntf=2, ntb=2, ntp=1, taup=1.0,
cut=8.0, iwrap=1, ig=-1,
ntpr=10000, ntwx=10000, ntwr=10000,
ntt=3, gamma_ln=5.0, temp0=300.0,
ntr=1, restraintmask=':1-873', restraint_wt=20.0,
ioutfm=1, barostat=2,
/
Step-6:MD1 simulation backbone restrained
&cntrl
imin=0, nstlim=100000, dt=0.002,
irest=1, ntx=5,
ntc=2, ntf=2, ntb=1,
cut=8.0, iwrap=1, ig=-1,
ntpr=500, ntwx=500, ntwr=500,
ntt=3, gamma_ln=5.0, temp0=300.0,
ntr=1,
restraintmask="(:1-838 & @CA,C,N,O) | (:839) | (:840 & @P2,O9,O10,O12,O4,O2,C5,C3,C1) | (:841-873 & @P,OP1,OP2,O3',O5',C3',C4',C5')",
restraint_wt=10.0,
ioutfm=1,
/
Step-7:MD1 simulation backbone restrained
&cntrl
imin=0, nstlim=100000, dt=0.002,
irest=1, ntx=5,
ntc=2, ntf=2, ntb=1,
cut=8.0, iwrap=1, ig=-1,
ntpr=500, ntwx=500, ntwr=500,
ntt=3, gamma_ln=5.0, temp0=300.0,
ntr=1,
restraintmask="(:1-838 & @CA,C,N,O) | (:839) | (:840 & @P2,O9,O10,O12,O4,O2,C5,C3,C1) | (:841-873 & @P,OP1,OP2,O3',O5',C3',C4',C5')",
restraint_wt=5.0,
ioutfm=1,
/
Step-8:MD1 simulation backbone restrained
&cntrl
imin=0, nstlim=100000, dt=0.002,
irest=1, ntx=5,
ntc=2, ntf=2, ntb=1,
cut=8.0, iwrap=1, ig=-1,
ntpr=500, ntwx=500, ntwr=500,
ntt=3, gamma_ln=5.0, temp0=300.0,
ntr=1,
restraintmask="(:1-838 & .CA,C,N,O) | (:839) | (:840 & @P2,O9,O10,O12,O4,O2,C5,C3,C1) | (:841-873 & @P,OP1,OP2,O3',O5',C3',C4',C5')",
restraint_wt=1.0,
ioutfm=1,
/
Step-9:MD1 simulation backbone restrained
&cntrl
imin=0, nstlim=100000, dt=0.002,
irest=1, ntx=5,
ntc=2, ntf=2, ntb=1,
cut=8.0, iwrap=1, ig=-1,
ntpr=500, ntwx=500, ntwr=500,
ntt=3, gamma_ln=5.0, temp0=300.0,
ntr=1,
restraintmask="(:1-838 & .CA,C,N,O) | (:839) | (:840 & @P2,O9,O10,O12,O4,O2,C5,C3,C1) | (:841-873 & @P,OP1,OP2,O3',O5',C3',C4',C5')",
restraint_wt=0.25,
ioutfm=1,
/
Step-10:MD1 simulation backbone restrained
&cntrl
imin=0, nstlim=100000, dt=0.002,
irest=1, ntx=5,
ntc=2, ntf=2, ntb=1,
cut=8.0, iwrap=1, ig=-1,
ntpr=500, ntwx=500, ntwr=500,
ntt=3, gamma_ln=5.0, temp0=300.0,
ntr=0,
ioutfm=1,
/
Step-11:good energy conservation, 2fs.
&cntrl
ntx=5, irest=1,
ntc=2, ntf=2, tol=0.000001,
nstlim=250000000,
ntpr=1000, ntwx=1000,
ntwr=10000,
dt=0.002, cut=8.0,
ntt=0, ntb=1, ntp=0, ntr=0,
ioutfm=1,
/
&ewald
dsum_tol=0.000001,
/
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======================================
Vojtech Mlynsky
Structure and Dynamics of Nucleic Acids
Institute of Biophysics of the Czech Academy of Sciences
Kralovopolska 135, 612 00, Brno, Czech Republic
======================================
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Received on Wed May 14 2025 - 13:00:02 PDT
