I’m trying to explore possible pathways for the exit of a ligand from the binding pocket of its receptor.
I’d appreciate any advice on the procedure that I’m following, which is as follows:
1. plan to repeat each SMD simulation 3-4 times from different starting coordinates taken from a 20ns MD trajectory. Is the number of repeats adequate?
2. I’m changing the distance of the centre of mass of my ligand to that of 10-14 residues in the proximity of the original position of the ligand in 1 Angstrom increments. Is incremental change of distance between the centers of mass of 1 Agstrom OK?
3. I’ve set rk2 = 500. Is this force acceptable?
I’d be most grateful for any comments on the 3 questions above as well as my smd input file below.
Thank you in advance
George
My pushing input is
&cntrl
imin=0,irest=1,ntx=5,
nstlim=1000000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000, ntwr=5000,
ntt=3, gamma_ln=2.0, ig=-1,
temp0=300.0,
jar=1,
/
&wt TYPE='DUMPFREQ', istep1=1, /
&wt TYPE='END', /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
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Received on Fri Oct 17 2014 - 13:00:02 PDT
