Maybe you need a dihedral restraint? A flipped ring isn't going to show up
strongly in an entire protein rmsd. Is the ring symmetric? Depending on the
details, the rmsd may go up as it flips, thus your current structure may be
a local minimum.
On Feb 23, 2016 6:26 AM, "Jean-Marc Billod" <jmbillod.cib.csic.es> wrote:
> It is indeed what I want and I understand that the ligand isn’t
> contributing a lot in the global rmsd average. Is there another way to
> force the flipping of the ring?
>
> > On 23 Feb 2016, at 12:14, Carlos Simmerling <carlos.simmerling.gmail.com>
> wrote:
> >
> > 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 - 04:30:04 PST
