Dear all,
I have problems with targeted MD.
I run targeted MD by using Amber18. I have performed 10-ns TMD. In my simulated system, there is a small molecule drug located at 24Å from the protein binding pocket (the crystal structure is a complex, and I pulled the ligand out of the pocket). As shown in the run command, I gave a reference structure (crystal sturucture postion) for this simulation. However, the TMD can't force the drug moving back to the protein binding pocket with rmsd =0. After the 10-ns TMD simulation, the trajectory show that the drug located at 14Å around the portein binding pocket.
For this problem, I want to know if there is something wrong with my input file syntax, or if my simulation time is not long enough? The input file (sander.in5) is shown below.
Run command:
mpirun -bind-to core -np 24 sander.MPI -O -i sander.in5 -o sander.out5 -p prmtop -c mdrest4 -r mdrest5 -x mdcrd5 -ref TMDcrd
Input file (sander.in5) :
Production 10 ns
&cntrl
imin=0,irest=0,
nstlim=5000000,dt=0.002,
temp0=300.0,ntt=3,gamma_ln=2.0,
ntc=2,ntf=2,ntx=1,nscm=0,tol=0.00001
cut=8.0,
ntpr=500,ntwx=2000,ntwv=0,ntwe=0,ntxo=1,iwrap=1,
ntb=2,ntp=1,pres0=1.0,taup=1.0,ntwr=500,
ipol=0,igb=0,
itgtmd=1,tgtmdfrc=0.005,ntr=0,tgtfitmask=":14,48,58,60,93,101,134,160,214-217",tgtrmsmask=":14,48,58,60,93,101,134,160,214-217"
/
&wt type='TGTRMSD', istep1=0,istep2=10000000,
value1=0.0, value2=0.0
/
&wt type='END'
/
Thank you very much!
Xiaodong
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Received on Thu Jan 14 2021 - 19:00:02 PST
