Hi,
You can reimage the trajectory to see if it is indeed an imaging
artifact. For example:
# Load topology
parm myparm.parm7
# Load trajectory
trajin mytraj.nc
# Re-image
autoimage
# Output trajectory
trajout imaged.nc
Also, certain commands (like distance, radial, hbond etc) support
imaging so there is no need to reimage beforehand. See the manual for
complete details. Hope this helps,
-Dan
On Mon, Dec 14, 2015 at 11:58 PM, Anasuya Dighe
<anasuya.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
>
> I am simulating a protein-ligand complex for a total of 100ns. The ligand in
> question is a peptide inhibitor, that is lodged in the catalytic cleft of the
> protein molecule. Upon completing the production run (spanning 100ns of data),
> I noticed some peculiar things happening in the trajectory.
> All of a sudden (at a random point in the simulation), the peptide inhibitor
> molecule was seen to be present at one end of the solvent box. It continued to
> be simulated there. The protein molecule was simulated at the other end of the
> box. Please mind the fact that this sudden behavior was not gradual in any
> sense ( i.e. the ligand was NOT exiting the catalytic cleft in a step-by-step
> fashion.)
> After a few (5-10) frames, the ligand went back to the cleft and this
> fluctuating behavior continued for around 10-12 ns, and after that the ligand
> was lodged in the cleft.The simulation otherwise completed after 100ns. Also
> please note that this behavior was NOT seen since the beginning of the
> simulation. In the beginning, the peptide was in the cleft. IT started all of a
> sudden at the 49th ns.
>
> I am quite puzzled at this picture. Is this an imaging issue?
> I am using the iwrap parameter as iwrap = 1
> The .in file for simulation is as follows :
>
> 1ns MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0, iwrap = 1,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2, ig = -1,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 500000, dt = 0.002,
> ntpr = 500, ntwx = 1000, ntwr = 100000
> /
>
> Please advice me about the steps to take in order to rectify this.
> Will something like this have an effect on the data analysis of the trajectory
> (using cpptraj)?
> Any special commands that i should use during cpptraj, in order to fix this?
>
> Thanks
> Anasuya Dighe
> C/o Prof. Saraswathi Vishveshwara,
> Lab No. 4, Molecular Biophysics Unit Annexe,
> Indian Institute of Science,
> Bangalore - 560012
>
>
> --
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>
>
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--
-------------------------
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 Tue Dec 15 2015 - 09:00:03 PST
