Dear Amber users,
I am attempt to save the first solvent shell waters by Ptraj.
First I used the watershell command to count the number of waters within
4 angstroms of the solute. the input file is :
trajin prod.mdcrd 1 1000 200
watershell :1-76 test.out lower 4.0
and the output file is
1 348 478
2 336 467
3 338 453
4 316 450
5 286 407
then I used the closest command to retain only the closest 348 waters to
the solute, the input file is:
trajin prod3.mdcrd 1 1000 200
closestwater 348 :1-76
trajout test_pdb pdb
and the Ptraj was successfully done:
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "/apps/amber11/exe/ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
MET GLN ILE PHE VAL LYS THR LEU THR GLY
LYS THR ILE THR LEU GLU VAL GLU PRO SER
ASP THR ILE GLU ASN VAL LYS ALA LYS ILE
GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN
GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU
GLU ASP GLY ARG THR LEU SER ASP TYR ASN
ILE GLN LYS GLU SER THR LEU HIE LEU VAL
LEU ARG LEU ARG GLY GLY WAT WAT WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
WAT WAT WAT WAT WAT
Setting box to be an exact truncated octahedron, angle is 109.471221
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin prod.mdcrd 1 1000 200
Checking coordinates: prod1.mdcrd
Rank: 0 Atoms: 15238 FrameSize: 370309 TitleSize: 81 NumBox: 3 Seekable 1
PTRAJ: closestwater 348 :1-76
Mask [:1-76] represents 1231 atoms
PTRAJ: trajout test_pdb pdb
prod.mdcrd: 1000 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 5 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (prod.mdcrd) is an AMBER trajectory (with box info) with 1000
sets (processing only 5)
OUTPUT COORDINATE FILE
File (test_pdb) is a PDB file
ACTIONS
1> CLOSESTWATERS: saving the 348 closest solvent molecules around
atoms :1-76
The current solvent mask is :77-4745
Processing AMBER trajectory file prod.mdcrd
PTRAJ: Successfully read in 5 sets and processed 5 sets.
Dumping accumulated results (if any)
However, when I check the output structure by VMD, I found there are a
lot of waters which are far very far from the solute. Could you tell me
where I have slipped up ?
Thank you very much for your help!
Best regards
Tong Zhu
--
Tong Zhu
------------------------------------------------------------------
State Key Laboratory of Precision Spectroscopy,
East China Normal University, Shanghai 200062, China and
Department of Physics, East China Normal University, Shanghai 200062, China
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Received on Mon Jun 27 2011 - 05:30:03 PDT
