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Imaging problem with ptraj

Thursday 13 November 2003

Description of the problem : i’m not able to image a dynamics run using water and counter-ions. DNA and water molecules are imaged, but not the counter ions.

Is it because their name is CIP ?

command: ptraj ../prm/helix.top2 ptraj_ions.in >&ptraj_ions.out

input file: ptraj.in

trajin dn300K15_c.Z
trajout dn300K.crd nobox
center :1-21 mass origin
image origin center
#rms first out rms_ions.dat time 1 :1-21
go

output file: ptraj.out

Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of @type)...
Read in residue labels...
Read in the residue to atom pointer list...
Read in bond parameters RK and REQ...
Read in angle parameters TK and TEQ...
Read in dihedral parameters PK, PN and PHASE...
Read in SOLTY...
Read in L-J parameters CN1 and CN2...
Read in info for bonds w/ hydrogen...
Read in info for bonds w/out hydrogen...
Read in info for angles w/ hydrogen...
Read in info for angles w/out hydrogen...
Read in info for dihedrals w/ hydrogen...
Read in info for dihedrals w/out hydrogen...
Read in excluded atom list...
Read in h-bond parameters: AG, BG, and HBCUT...
Read in atomic symbols (types)...
Read in tree information...
Read in the JOIN info...
Read in the IROTAT info...
Read in box information...
C5   T    C    T    GDP  GDP  T    C    T    C3  
G5   A    G    A    C    C    A    G    A    G3  
PTP  CIP  CIP  CIP  CIP  CIP  CIP  CIP  CIP  CIP
CIP  CIP  CIP  CIP  CIP  CIP  WAT  WAT  WAT  WAT
WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT
...
WAT
Scanning Box
Successfully completed readParm.

PTRAJ: Processing input file...
      Input is from file ptraj_ions.in

PTRAJ: trajin dn300K15_c.Z

PTRAJ: trajout dn300K.crd nobox

PTRAJ: center :1-21 mass origin
Mask [:1-21] represents 658 atoms

PTRAJ: image origin center
Mask [*] represents 15508 atoms

PTRAJ: go

PTRAJ: Successfully read the input file.
      Coordinate processing will occur on 200 frames.
      Summary of I/O and actions follows:

INPUT COORDINATE FILES
 File (dn300K15_c.Z) is an AMBER trajectory (with box info) with 200 sets

OUTPUT COORDINATE FILE
 File (dn300K.crd) is an AMBER trajectory

ACTIONS
 1>  CENTER to origin via center of mass, atom selection follows :1-21
 7>  IMAGE  by molecule to origin using the center of mass, atom selection   * (All atoms are selected)


Processing AMBER trajectory file dn300K15_c.Z
Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 .................................................
Set    200

PTRAJ: Successfully read in 200 sets and processed 200 sets.
      Dumping accumulated results (if any)

But the counter-ions are not imaged (blue spheres) although water molecules are, as illustrated by the image.

Solution:

Thanks to Dr. T. E. Cheatham, i could found out what was wrong in my input and correct it. The difference is :

trajin dn300K15_c.Z
trajout dn300K.crd nobox
center :1-21 mass origin

image origin center byres :CIP com :1-21

image origin center
#rms first out rms_ions.dat time 1 :1-21
go

Like this, counter ions are imaged explicitly and get back in the correct box.

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