Hi,
I recommend trying the 'autoimage' command in cpptraj.
-Dan
On Friday, February 22, 2013, ET wrote:
> Hi all,
> I'm running a long MD simulation of 100ns of a ligand bound to a protein
> using amber 10. I turned iwrap=1 to avoid the simulation stalling due
> to precision errors.
>
>
> ##################
> production run infile
> &cntrl
> nstlim=2000000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=500, ntwx=500,
> temp0=300.0, ntt=1, tautp=2.0, iwrap=1, ig=-1
>
> ntb=2, ntp=1,
>
> ntc=2, ntf=2,
>
> nrespa=1,
> &end
> #################
>
> I ran a quick test measuring the distance from the hydroxyl group of the
> ligand which a primary alcohol with a cis-3-4 double bond to Tyr120. The
> distances seemed quite large (distance graphs for one of the ligands
> attatched). When I check the trajectories with vmd or chimera, the ligand
> does not seem to be behaving properly: either coming out of the pocket or
> getting stuck on part of the protein (when visualized with vmd).
>
> I'm pretty sure this is an imaging problem. I have more simulations where
> the ligand comes out of the pocket for a some frames then goes back in. the
> larger image enclosed illustrates the issue across 3 repeats of 4 different
> ligands bound to the same protein. Each graph measures distance between the
> ligand and Tyr120 of a different trajectory. The protein MUP is like a
> barrel and the ligand is expected to be relatively mobile within the
> pocket, but prob not to this extent.
>
> I have looked through the archives and tried applying the following ptraj
> imaging commands with no success;
>
> The protein residues = 1-157
> The ligand = 158
> #############
> trajin md_1.crd
> center :1-157 mass origin
> image :1-157 origin center bymask :1-157 familiar
> center :1-158 mass origin
> image :1-158 origin center bymask :1-158 familiar
> trajout md_1_manImaged.ncdf netcdf
> #############
>
> Zipped Files containing the first 300 frames of a original (before imaging)
> trajectory and topology files can be downloaded from the following links:
>
> 1) 3c6-ligand-protein:
> https://dl.dropbox.com/u/12686110/04_3c6.zip
>
>
> Any help anyone could offer to solve this issue would be greatly
> appreciated.
>
> Best regards,
> ET
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Feb 22 2013 - 12:30:02 PST
