Your fit and rmsd mask are for all non water heavy atoms. Is that what you
want? If the ligand is a small part of the system it won't contribute much
to the average in the rmsd.
On Feb 23, 2016 4:45 AM, "Jean-Marc Billod" <jmbillod.cib.csic.es> wrote:
> 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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>
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Received on Tue Feb 23 2016 - 03:30:04 PST
