Hi
Can you try the most updated cpptraj (ambertools16) and let us know what happens.
Hai
> On Sep 8, 2016, at 11:05 AM, dhanasekar.mbu.iisc.ernet.in wrote:
>
> Hi,
>
> I am running prot+ligand simulation for a couple of systems for understanding
> ligand bound conformational changes. (I have used standard Amber14 protocols for
> setting up the system, minimization, equilibration, etc.)
>
> I have generated 100ns production run data and am using cpptraj version 14.25
> for the analysis.
> I had earlier run rmsd calculations for all systems using the following script :
>
> strip :WAT
> strip :Na+
> center :1-250 mass
> autoimage
> rms first out rmsd.dat :1-250.CA
> atomicfluct out Per-res-fluct.dat :1-250 byres
> atomicfluct out CA-fluct.dat @CA byatom
> go
>
> rmsd was below 2Å and system appeared stable.
>
> I have to re-run rmsd again, and am facing some problems inspite of using same
> crd files, same prmtop file and same rmsd.in file :
>
> 1) RMSD data shows RMS as high as 25-45Å for a selected number of snapshots
> after an interval of 50 frames. I find this very weird since I used the same
> data ( crd files) a few days back with the same prmtop file and with the same
> cpptraj code, but did not see any of this earlier.
> No errors were reported during cpptraj analysis. After data has been generated,
> it looks something like.
>
> When visualised in VMD, I do not see any drastic changes in the prot structure.
> Everything appears to be OK.
>
> Is there any way to rectify this ? What seems to be the problem? Is this an
> imaging issue or have the trajectories become corrupted? If so, please suggest
> remedial measures.
>
> Thank you.
>
> Regards,
> B.K. Dhanasekaran
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> <old_rmsd_result.jpg>
> <new_rmsd_result.jpg>
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Received on Thu Sep 08 2016 - 10:30:03 PDT
