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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue Feb 23 2016 - 04:00:04 PST
