AMBER Archive (2008)

Subject: AMBER: ptraj closest command

From: steinbrt_at_rci.rutgers.edu
Date: Mon Nov 17 2008 - 10:14:11 CST

Hi Amber users,

Im having trouble using ptraj's closest command to select a few water
molecules closest to a solute. Heres my input:

--------------------------------------------------------------
trajin ph0_wat_pro.crd_img
solvent byres :WAT
closest 3 @1
trajout ph0_wat_pro.crd_img_3w pdb
--------------------------------------------------------------

the coordinate file read is centered on molecule 1 and imaged.
ptraj runs fine and gives output that looks unsuspicious:

--------------------------------------------------------------
PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin ph0_wat_pro.crd_img
  Checking coordinates: ph0_wat_pro.crd_img

PTRAJ: solvent byres :WAT
Mask [:WAT] represents 2259 atoms
       Searching for solvent by mask :2-754

PTRAJ: closest 3 @1
Mask [@1] represents 1 atoms

PTRAJ: trajout ph0_wat_pro.crd_img_3w pdb

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 1000 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (ph0_wat_pro.crd_img) is an AMBER trajectory (with box info) with
1000 sets

OUTPUT COORDINATE FILE
  File (ph0_wat_pro.crd_img_3w) is a PDB file

ACTIONS
  1> CLOSESTWATERS: saving the 3 closest solvent molecules around atoms
:1_at_P1
      The current solvent mask is :2-754

Processing AMBER trajectory file ph0_wat_pro.crd_img
....
-----------------------------------------------------------

but the pdb files produced do not contain the closest waters:

e.g.:

REMARK 1 PDB file generated by ptraj (set 1000)
ATOM 1 P1 po4 1 0.008 0.012 0.000 0.00 0.00
[...]
TER 0 0
ATOM 12 O WAT 4 12.041 -7.377 -10.470 0.00 0.00
ATOM 13 H1 WAT 4 12.964 -7.450 -10.712 0.00 0.00
ATOM 14 H2 WAT 4 12.043 -6.842 -9.677 0.00 0.00

Visual inspection shows that there are water molecules much closer to the
solute than the ones ptraj actually picks (the solute is small and the
closest waters are no more than 3-4A away).

Is there anything obvious I overlooked? Any suggestions what Im doing
wrong? (Using the noimage command doesnt change anything, neither does
picking the full residue :1 as mask in closest)

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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