Dear all,
I have performed tMD with AMBER12 using the following script:
&cntrl
nstlim = 2500000, dt = 0.002,
ntx = 1, irest = 0,
ntpr = 500, ntwr = 500, ntwx = 500,
tempi = 300., temp0 = 300.,
cut = 15.0,
ntt = 1,
ntb = 2, ntp = 1,
ntc = 2, ntf = 2,
nscm = 0,
itgtmd = 1, tgtmdfrc = 0.25,
tgtrmsd = 4.9,
tgtfitmask="!.H= & !:WAT",
tgtrmsmask="!.H= & !:WAT",
nmropt=1,
/
&wt
TYPE='TGTRMSD', istep1=1, istep2=400000,
value1 = 4.9, value2 = 4.2,
/
&wt
TYPE='TGTRMSD', istep1=400001, istep2=800000,
value1 = 4.2, value2 = 3.0,
/
&wt
TYPE='TGTRMSD', istep1=800001, istep2=1200000,
value1 = 3.000, value2 = 2.0,
/
&wt
TYPE='TGTRMSD', istep1=1200001, istep2=1600000,
value1 = 2.000, value2 = 1.0,
/
&wt
TYPE='TGTRMSD', istep1=1600001, istep2=2000000,
value1 = 1.0, value2 = 0.0,
/
&wt
TYPE='TGTRMSD', istep1=2000000, istep2=2500000,
value1 = 0.0, value2 = 0.0,
/
I used two crystal structures with the ligand inside the binding pocket; in the final crystal, one aromatic ring of the ligand is flipped compared to the first crystal. I performed the simulation and I had no error but I realized that the ligand does not undergo the flipping... basically only the conformation of the protein changes but not the one of the ligand. In fact, the last RMSD is not 0:
R M S F L U C T U A T I O N S
NSTEP = 2500000 TIME(PS) = 5025.000 TEMP(K) = 0.88 PRESS = 107.6
Etot = 238.4099 EKtot = 123.0485 EPtot = 268.7670
BOND = 32.9511 ANGLE = 48.2236 DIHED = 30.4487
1-4 NB = 18.4036 1-4 EEL = 73.6341 VDWAALS = 195.7646
EELEC = 272.2557 EHBOND = 0.0000 RESTRAINT = 210.8199
EAMBER (non-restraint) = 57.9471
EKCMT = 94.1915 VIRIAL = 1587.6094 VOLUME = 717.5546
Density = 0.0011
Ewald error estimate: 0.4427E-04
Current RMSD from reference: 0.972
Current target RMSD: 0.000
Am I doing anything wrong? Any suggestions?
Thanks a lot,
Jean-Marc
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Received on Tue Feb 23 2016 - 02:00:04 PST
