Re: [AMBER] Problem with CRD files

From: Nhai <nhai.qn.gmail.com>
Date: Thu, 8 Sep 2016 13:35:36 -0400

By the way, are you sure you used identical input?

In the first figure, you have 100 ns while in the 2nd one you have 95 ns. Can you attach cpptraj log for 2nd run?

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
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> <old_rmsd_result.jpg>
> <new_rmsd_result.jpg>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 08 2016 - 11:00:02 PDT
Custom Search