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!
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
>>
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>>
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--
------------------------------------------------------------------------
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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Received on Thu Jul 12 2012 - 12:00:04 PDT
