I am attempting to use the image command to have a correct visual
representation of the molecular system on which I have executed molecular
dynamics using DESMOND. I am working with a protein-ligand complex in
which the protein has two pieces (the first piece has residue numbers going
from 5 to 170, while the second runs from 184 to 352). Consequently, it
appears during the simulation that one of the pieces has "floated away" and
hence the need to image.
the commands I issued were as follows:
<
http://www.putlocker.com/file/1B3B80AEEE189F23>shashi.truffle:/u2/shashi_local/P38/DESMOND_MD_JUN27$
cpptraj
CPPTRAJ: Trajectory Analysis. V13.8b
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> parm reference.pdb
[parm reference.pdb]
reference.pdb: determining bond info from distances.
reference.pdb: 2731 bonds to hydrogen, 2789 other bonds.
reference.pdb: determining molecule info from bonds.
> trajin sampletrj1.pdb
[trajin sampletrj1.pdb]
[sampletrj1.pdb] contains 11 frames.
> image com :5-170 :184-352
[image com :5-170 :184-352]
> go
the output that was generated (seems like a failed attempt)
INPUT TRAJECTORIES:
[sampletrj1.pdb] is a PDB file, Parm reference.pdb (reading 11 of 11)
Coordinate processing will occur on 11 frames.
PARAMETER FILES:
0: reference.pdb, 5472 atoms, 352 res, box: None, 19 mol, 11 frames
REFERENCE COORDS:
No frames defined.
OUTPUT TRAJECTORIES:
No files.
ACTIONS: Initializing 1 actions:
0: [image com :5-170 :184-352]
IMAGE: To box center based on first atom position using atoms in mask
:5-170
Warning: [image] Not all arguments handled: [ com :184-352 ]
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [reference.pdb]: Setting up 1 actions.
0: [image com :5-170 :184-352]
Warning: Image::setup: Parm reference.pdb does not contain box information.
Warning: Setup failed for [image com :5-170 :184-352]: Skipping
----- [sampletrj1.pdb] (1-11, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 11 frames and processed 11 frames.
ACTION OUTPUT:
DATASETS:
There are no data sets set up for analysis.
DATASETS AFTER ANALYSIS:
There are no data sets set up for analysis.
the reference PDB has its top few lines as follows:
CRYST1 91.370 64.892 72.857 90.00 90.00 90.00 P 1 1
ATOM 1 N ARG A 5 31.650 -8.035 -7.270 0.00 0.00
C2 N
ATOM 2 CA ARG A 5 31.156 -6.847 -6.574 0.00 0.00
C2 C
ATOM 3 C ARG A 5 31.252 -5.644 -7.535 0.00 0.00
C2 C
ATOM 4 O ARG A 5 32.293 -5.499 -8.179 0.00 0.00
C2 O
ATOM 5 CB ARG A 5 31.946 -6.658 -5.253 0.00 0.00
C2 C
ATOM 6 CG ARG A 5 31.489 -5.489 -4.361 0.00 0.00
C2 C
ATOM 7 CD ARG A 5 32.376 -5.338 -3.115 0.00 0.00
C2 C
the PDB file of the trajectory was generated using VMD in which I read in
the DESMOND trajectories after input of the reference CMS molecule.
Any clues on what is the correct way to go about this?
thanks,
Shashi Rao
image com :5-170 :184-352
However, the output looked as follows:
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Tue Jan 15 2013 - 11:00:02 PST
