Hello,
I am currently trying to perform steered MD using amber so as to push a
RNA micro helix to a protein's pocket with known binding site (Pushing
from a distance of 14.1 Å to 5.1 Å). The steered MD using .RST file is
tried so far but I am unable to change the CV. The inputs are attached
here with
For SMD:
&cntrl
imin=0,
irest=1,
ntx=5,
nstlim=50000000,
dt=0.002,
ntc=2, ntf=2,
cut=8.0,
ntb=2,
ntp=1, taup=2.0,
ntpr=1000,
ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
jar=1,
nmropt=1,
/
&wt type='DUMPFREQ', istep1=1000 /
&wt type='END' /
DISANG=smd1.RST
DUMPAVE=force_datac32.dat
For .RST :
&rst
iat=6160,2493,
r1=0.0, r2=5.1, r3=5.1, r4=50.0,
rk2=0.0, rk3=10.0,
/
This does not worked well for the system and increasing restraints
destabilizing the system.
Can anyone tell me the about the possibility of this .RST based method?
To change the CV the I read that patching of PLUMED with AMBER is
needed. If anyone did the same it will be much helpful to get the
insights about patching and further processing with PLUMED-AMBER SMD.
Regards,
Sidharth.E.K.
PhD Scholar
IIT Bombay
24d0242.iitb.ac.in
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Received on Thu May 15 2025 - 05:00:02 PDT
