[AMBER] tMD with ligand

From: Jean-Marc Billod <jmbillod.cib.csic.es>
Date: Tue, 23 Feb 2016 10:45:45 +0100

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
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