Hi,
You are writing your output trajectory with box coordinates, but my guess
is that GKDk5.H.top has none. Box coordinate detection in ASCII
trajectories can be sometimes problematic with ASCII trajectories. Try
writing your output trajectory in NetCDF format instead, e.g.:
trajout ./GKDk5.0-100ns.NoWAT.nc
That should fix things.
-Dan
On Wed, Jun 17, 2015 at 2:33 PM, Yin, Guowei <guowei_yin.med.unc.edu> wrote:
> Hi,
>
> I have 3 trajectory files which are written for simulations "0-50ns",
> "50-95ns" and "95-100ns". I want to first link them one to other as a
> chronological order into one trajectory file which contain "0-100ns". It
> should be in total 50003 frames in the combined trajectory files. However,
> when I calculated rmsd based on this combined trajectory, it's recognized
> as only 40485 frames. Before I use ptraj, it works well, but now I use
> cpptraj. Not sure if this change makes different. Could anyone help me
> check? Thank you.
>
> You can find some details as below:
>
> the script I used to combine multiple trajectories:
> cpptraj -p ../GKDk5.S.top <<eof
> trajin ../GKDk5.50ns.mdcrd
> trajin ../GKDk5.100ns.mdcrd
> trajin ../GKDk5.100ns+.mdcrd
> strip :WAT,Na+,Cl-
> trajout ./GKDk5.0-100ns.NoWAT.mdcrd
> go
> eof
>
> Below is the process of cpptraj and rmsd calculation:
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM '../GKDk5.S.top' (1 actions):
> 0: [strip :WAT,Na+,Cl-]
> Stripping 25871 atoms.
> Stripped parm: '../GKDk5.S.top', 2679 atoms, 168 res, box: Trunc.
> Oct., 3 mol
> ----- GKDk5.50ns.mdcrd (1-25000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- GKDk5.100ns.mdcrd (1-23492, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- GKDk5.100ns+.mdcrd (1-1511, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 50003 frames and processed 50003 frames.
> TIME: Trajectory processing: 250.3706 s
> TIME: Avg. throughput= 199.7160 frames / second.
>
>
> RMSD script:
> cpptraj ../GKDk5.H.top <<eof
> trajin ./GKDk5.0-100ns.NoWAT.mdcrd
> reference ../GKDk5.H.pdb
> rms reference mass out GKDk5.0-100ns.all.rmsd
> rms reference mass out GKDk5.0-100ns.CA.rmsd .CA
> go
> eof
>
> RMSD prcess:
> INPUT TRAJECTORIES:
> 0: 'GKDk5.0-100ns.NoWAT.mdcrd' is an AMBER trajectory, Parm ../GKDk5.H.top
> (reading 40485 of 40485)
> Coordinate processing will occur on 40485 frames.
>
> REFERENCE FRAMES (1 total):
> 0: '../GKDk5.H.pdb', frame 1
> Active reference frame for masks is 0
> TIME: Run Initialization took 0.0001 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM '../GKDk5.H.top' (2 actions):
> 0: [rms reference mass out GKDk5.0-100ns.all.rmsd ]
> Target mask: [*](3309)
> 1: [rms reference mass out GKDk5.0-100ns.CA.rmsd .CA]
> Target mask: [.CA](166)
> ----- GKDk5.0-100ns.NoWAT.mdcrd (1-40485, 1) -----
>
> Best,
> Guowei
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 18 2015 - 08:30:04 PDT
