AMBER: ptraj closest command

From: <>
Date: Mon, 17 Nov 2008 11:14:11 -0500 (EST)

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:

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

  File (ph0_wat_pro.crd_img_3w) is a PDB file

  1> CLOSESTWATERS: saving the 3 closest solvent molecules around atoms
      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:


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,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Dec 05 2008 - 15:45:41 PST
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