Hi,
It's difficult to know exactly what is going on without knowing more
about your original trajectory, but based on the files you provided
something is definitely strange. As far as I can tell, the imaging is
correct, and there is indeed a clash in that first frame (from
md41.trj). If I use the topology and trajectory you provided and strip
away the water, postprocessing (imin = 5) results in the following
energies (extra whitespace removed):
minimizing coord set # 1
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.1259E+12 9.3729E+11 4.6660E+13 H3 3719
BOND = 692.8319 ANGLE = 1961.5400 DIHED = 2516.4780
VDWAALS = ************* EEL = -16107.8991 HBOND = 0.0000
1-4 VDW = 845.7206 1-4 EEL = 9394.0279 RESTRAINT = 0.0000
minimization completed, ENE= 0.11258956E+13 RMS= 0.937291E+12
|Largest sphere to fit in unit cell has radius = 28.605
minimizing coord set # 2
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -2.3365E+03 1.9499E+01 1.3309E+02 CD 1537
BOND = 690.6412 ANGLE = 1985.1327 DIHED = 2527.4048
VDWAALS = -1711.2791 EEL = -16089.8524 HBOND = 0.0000
1-4 VDW = 865.1406 1-4 EEL = 9396.2972 RESTRAINT = 0.0000
minimization completed, ENE= -.23365150E+04 RMS= 0.194992E+02
Can you send me (off-list) the mdout file that corresponds to
md41.trj? Maybe there is some clue in there that will point to what is
happening...
-Dan
On Mon, Jul 2, 2012 at 10:40 AM, Harald Lanig
<harald.lanig.chemie.uni-erlangen.de> wrote:
> Dear Carlos, dear AMBER list followers,
>
> thank you for the fast reply!
> Yes, I checked the archive carefully before submitting the question to
> the list, but the problem still remains. Therefore I decided to provide
> some example files for illustration.
>
> The file two_snaps.trj contains two snapshots extracted from a long PBC
> simulation in a truncated octahedral water box recorded with iwrap=1,
> simply to avoid format errors in the .rst file.
> It was generated by the following ptraj script:
>
> ptraj ../cl5_cspb_b1.top
>
> trajin ../md41.trj 1 1 # takes only the first snap
> trajin ../md83.trj 1 1
>
> trajout ./two_snaps.trj
> go
>
> The system contains a protein 1-233, a ligand 234, two anions 235-236
> and water. Then, I tried to image this 2-snap trajectory by
>
> ptraj ../cl5_cspb_b1.top
>
> trajin ./two_snaps.trj
>
> center :1-233 origin
> image origin center familiar
>
> trajout snap_img.pdb pdb
> go
>
> resulting in the two PDB files also provided in the attachment. The
> problem I am facing is that in the first PDB file the ligand 234 clashes
> into the protein backbone, whereas in the second PDB file everything is
> as expected. This is somehow surprising to me, because also for the
> first snap there should be the possibility to generate a protein-ligand
> complex without any van-der-Waals conflicts. The energy contributions
> during the simulation show no problems at all. Is there a reason for the
> fact that parts of the simulation can be imaged correct, and other parts
> not? Running the same simulation with iwrap=0 stops after a few hundred
> ns because of format problems. I avoided any RMS fittings, because they
> also change the orientation of the box and affect, according to earlier
> postings, the results of the image command.
>
> Thank you very much for helping me!
>
> Because the archive with the files is too large to attach it to this
> email and distribute it to the list members, here is a link to download
> it from my web server:
>
> http://www.chemie.uni-erlangen.de/lanig/img_problem.zip
>
> Best wishes,
> -Harald
>
>
>
>
>
>
> Am 29.06.2012 16:43, schrieb Carlos Simmerling:
> > yes, the correct way is to use the ptraj center and image commands.
> look in
> > the archives for many examples, and if you still cant' get it to
> work, send
> > your ptraj script. do check the archives first, though...
> >
> > On Fri, Jun 29, 2012 at 10:42 AM, Harald Lanig <
> > harald.lanig.chemie.uni-erlangen.de> wrote:
> >
> >> Dear Amber users,
> >>
> >> upon analysing a PBC simulation with a ligand non-covalently interacting
> >> with a protein, I observed large jumps of tenth of angstroms when
> >> plotting the distances between the center of masses of the protein and
> >> the ligand. I attributed this to jumps caused by periodic boundary
> >> conditions, placing e.g. the ligand in a different imaginary box than
> >> the protein. Extracting one snap out of the trajectory clearly shows
> >> that the ligand is located side-by-side to the protein, separated by
> >> more than 40 angstrom.
> >> Trying to image the ligand back into the box with the protein (using
> >> ptraj by centering to the protein and imaging only the ligand) resulted
> >> in a complex where the ligand clashes into the protein structure.
> >> My question is:
> >> Is this the correct way to re-generate a "normal" protein-ligand complex
> >> within the same box e.g. to visualize the interactions? Is there
> >> something wrong with my considerations or can you recommend me a
> >> procedure to make "real" complexes for visualisation.
> >>
> >> Thanks a lot for any advice!
> >>
> >> Best wishes,
> >> -Harald--
> ------------------------------------------------------------------------
> Dr. Harald Lanig Universitaet Erlangen/Nuernberg
> Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen
>
> Phone +49(0)9131-85 26525 harald DOT lanig AT chemie.uni-erlangen.de
> Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig
> ------------------------------------------------------------------------
>
>
>
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--
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Lab Specialist
Department of Medicinal Chemistry
University of Utah
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Received on Fri Jul 13 2012 - 10:00:03 PDT
