Hi,
Likely your trajectory files 'md_simulation9.mdcrd.gz' and
'md_simulation10.mdcrd.gz' have been either truncated or corrupted in
some way. If they are truncated, cpptraj may have a better chance of
reading the good frames if you first decompress (gunzip) the two
trajectories. If the corruption has happened in the middle of one or
both of the trajectories recovery of the data may not be possible. In
the future I recommend that you use the NetCDF trajectory and restart
formats (ioutfm=1 and ntxo=2 respectively) to avoid such issues.
Hope this helps,
-Dan
On Sun, Mar 6, 2016 at 11:52 PM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> I have performed 5 ns. I have run total 10 jobs, one job is equal to o.5 ns. After 4 ns (md run = 9) my was killed. I started again. When 5 ns simultion completed, I have plotted rmsd graph using cpptraj.
> INPUT TRAJECTORIES:
> 0: 'md_simulation1.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
> 1: 'md_simulation2.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
> 2: 'md_simulation3.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
> 3: 'md_simulation4.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
> 4: 'md_simulation5.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
> 5: 'md_simulation6.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
> 6: 'md_simulation7.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
> 7: 'md_simulation8.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box) (reading 2500 of 2500)
> 8: 'md_simulation9.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box), unknown #frames, start=0 offset=1
> 9: 'md_simulation10.mdcrd.gz' is an AMBER trajectory, Parm apo.prmtop (Orthogonal box), unknown #frames, start=0 offset=1
> Total number of frames is unknown.
> TIME: Run Initialization took 0.0015 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> In last two mdcrd.gz files number of frame is unknow, (Orthogonal box), unknown #frames, start=0 offset=1). It effects rmsd plot.
>
>
> Progress: '+' = 200 iterations.
> ----- md_simulation9.mdcrd.gz (1-EOF, 1) -----
> 0
> Progress: '+' = 200 iterations.
> ----- md_simulation10.mdcrd.gz (1-EOF, 1) -----
>
> I can not understand this error. Kindly help me in this regard.
> Thank you.
> Best Regards, Saman Yousuf AliJunior Research Fellow,
> | Lab No. P-133, Computational Chemistry Laboratory
> Dr. Panjwani Center for Molecular Medicine & Drug Research,
> International Center for Chemical & Biological Sciences,
> University of Karachi – 75270.Karachi-Pakistan.
>
> Contact No:
> Office (92-21) 111222292 (Ext 309)
> Email ID: saman.yousufali64.yahoo.com
> saman.ali.iccs.edu
>
> |
>
> _______________________________________________
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 07 2016 - 08:00:03 PST
