Do you have more than 1 molecule? If so, this is a common question, look at
imaging options in cpptraj.
On Mar 10, 2015 5:47 AM, "Anasuya Dighe" <anasuya.mbu.iisc.ernet.in> wrote:
>
> Dear Amber Users,
> I have run a 100ns MD of a protein. Following is the .in file i was
> using the
> run the simulation
> ----
> 100ps MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,ig = -1,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 50000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
> ----
> However, when I am analysing the trajectories, I am facing some issues.
> (1) After completion of the production run of 100ns, I am using the first
> frame
> of the production dynamics to obtain a RMSD using cpptraj. The following
> are
> the commands that I am using for the same.
>
> ---RMSD.in---
> trajin ./1abc-md1.crd
> .
> .
> .
> trajin ./1abc-md1000.crd
> strip :WAT
> center :1-325 mass origin
> image origin center familiar
> rms first out rms-test.dat :1-325.CA
> atomicfluct out per-res-fluct.dat :1-325 byres
> go
> ------------
>
> The resulting output file is showing a blowup of rmsd to 19.6556 Angstrom
> for
> almost 19 frames in the simulation around the 80th ns.
> (please see data below) The rest of the RMSD data, does not show any such
> drastic deviations. It stays in the 2.0 to 3.0 Angstrom range.
> ----RMSD DATA---
> 399601 2.7011
> 399602 2.6962
> 399603 2.7055
> 399604 2.6971
> 399605 2.7137
> 399606 2.7178
> 399607 2.6781
> 399608 2.6682
> 399609 2.6534
> 399610 2.6402
> 399611 19.6556 <---
> 399612 19.6556 <---
> 399613 19.6556 <---
> 399614 19.6556 <---
> 399615 19.6556 <---
> 399616 19.6556 <---
> 399617 19.6556 <---
> 399618 19.6556 <---
> 399619 19.6556 <---
> 399620 19.6556 <---
> 399621 19.6556 <---
> 399622 19.6556 <---
> 399623 19.6556 <---
> 399624 19.6556 <---
> 399625 19.6556 <---
> 399626 19.6556 <---
> 399627 19.6556 <---
> 399628 19.6556 <---
> 399629 19.6556 <---
> 399630 2.5816
> 399631 2.5835
> 399632 2.5920
> 399633 2.5742
> 399634 2.5583
> 399635 2.5812
> ------
> What could be happening here ? Why this drastic difference in the RMSD ?
> What
> was peculiar is, nowhere else in the simulation was there such a leap in
> RMSD.
>
> (2) When I traced back the frames to the corresponding MD simulation, I
> tried
> visualizing the relevant mdcrd file in VMD. This produced visualization of
> only
> the first nine frames i.e from frame number 399601-399610. At the next
> step, VMD
> crashed. Why is this happening ?
>
> (3) Next to probe further, I tried to see whether there were some issues
> with
> the protein structure in these frames. When I tried using cpptraj for the
> extraction of PDB files for these frames, I got the following error
> message :
>
> ----------
> 1uh7-wat-md801.crd (1-500, 1)
> 0% Warning: For PDB, box coords for first frame only will be written to
> CRYST1.
> Warning: Frame 11 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 12 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 13 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 14 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 15 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 16 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 17 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 18 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 19 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 20 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 21 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 22 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 23 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 24 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 25 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 26 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 27 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 28 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 29 coords 1 & 2 overlap at origin; may be corrupt.
> 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----------
> Are these two issues related ?
> What seems to be going wrong here in the simulation? What can i do to
> rectify
> this error?
> Please help.
>
> Regards,
> Anasuya Dighe
> Indian Institute of Science,
> Bangalore,
> INDIA
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
> _______________________________________________
> 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 Tue Mar 10 2015 - 03:30:02 PDT
