Hi Dan,
I tried doing that on our amber 12 installation. Unfortunately, it did not
make a difference.
best regards,
ET
On 22 February 2013 20:19, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 22 2013 - 14:00:02 PST
