Hi,
Based on visualization of the files you provided after 'autoimage',
this is not an imaging issue: the ligand just falls out of the binding
pocket.
-Dan
On Fri, Feb 22, 2013 at 2:45 PM, ET <sketchfoot.gmail.com> wrote:
> 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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--
-------------------------
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 - 14:30:03 PST
