Dear All,
I am trying to use the first frame from a binpos trajectory as the
reference frame for use within ptraj's rms function. It seems to
initially process the binpos file as the reference file, but then later
in execution, it complains that it is "missing a reference structure".
If one repeats this process, but uses a pdb for the reference, it works
fine.
Here's the ptraj script I'm using
PTRAJ="/netbin/x86_64/amber-9.24/exe/ptraj"
$PTRAJ ../NDP/1_Initial_Water_Minimisation/1HLD_NAD+_Pav_Params.prmtop
<< EOF
reference
../NAD/5_Production_300K_10ps/1HLD_NAD_BZO_prod_300K_both_stages_CENTERED.binpos
#reference
../NAD/5_Production_300K_10ps/1HLD_NAD_BZO_prod_300K_both_stages_CENTERED_1.pdb
trajin
../NDP/5_Production_300K_10ps/1HLD_NDP_BZA_prod_300K_10ps_CENTERED.binpos
strip :WAT
rms reference out rms.dat
EOF
The above is executed twice, but swapping the "#" on the reference line.
These are snippets from the two outputs:
GOOD (reference = pdb file)
=====
PTRAJ: Processing input from "STDIN" ...
PTRAJ: reference
../NAD/5_Production_300K_10ps/1HLD_NAD_BZO_prod_300K_both_stages_CENTERED_1.pdb
Reading string (ATOM 2 H1 SER 1 53.949 117.399 37.206
0.00 0.00
) R = -1073759536
Processing PDB file
../NAD/5_Production_300K_10ps/1HLD_NAD_BZO_prod_300K_both_stages_CENTERED_1.pdb
PTRAJ: trajin
../NDP/5_Production_300K_10ps/1HLD_NDP_BZA_prod_300K_10ps_CENTERED.binpos
Checking coordinates:
../NDP/5_Production_300K_10ps/1HLD_NDP_BZA_prod_300K_10ps_CENTERED.binpos
PTRAJ: strip :WAT
Mask [:WAT] represents 69249 atoms
PTRAJ: rms reference out rms.dat
Mask [*] represents 11448 atoms
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 5000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File
(../NDP/5_Production_300K_10ps/1HLD_NDP_BZA_prod_300K_10ps_CENTERED.binpos)
is a BINPOS file with 5000 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
REFERENCE FILE
File
(../NAD/5_Production_300K_10ps/1HLD_NAD_BZO_prod_300K_both_stages_CENTERED_1.pdb)
is a PDB file
ACTIONS
1> STRIP: 69249 atoms will be removed from trajectory: :761-23843
7> RMS to reference structure
(../NAD/5_Production_300K_10ps/1HLD_NAD_BZO_prod_300K_both_stages_CENTERED_1.pdb)
using no mass weighting
Dumping RMSd vs. time (with time interval 1.00) to a file named
rms.dat
Atom selection follows * (All atoms are selected)
BAD (reference = binpos)
====
PTRAJ: Processing input from "STDIN" ...
PTRAJ: reference
../NAD/5_Production_300K_10ps/1HLD_NAD_BZO_prod_300K_both_stages_CENTERED.binpos
Processing BINPOS file
../NAD/5_Production_300K_10ps/1HLD_NAD_BZO_prod_300K_both_stages_CENTERED.binpos
PTRAJ: trajin
../NDP/5_Production_300K_10ps/1HLD_NDP_BZA_prod_300K_10ps_CENTERED.binpos
Checking coordinates:
../NDP/5_Production_300K_10ps/1HLD_NDP_BZA_prod_300K_10ps_CENTERED.binpos
PTRAJ: strip :WAT
Mask [:WAT] represents 69249 atoms
PTRAJ: rms reference out rms.dat
WARNING in ptraj(), rms to reference: missing reference structure.
Set this prior to this rms with the command "reference"
Ignoring command...
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 5000 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File
(../NDP/5_Production_300K_10ps/1HLD_NDP_BZA_prod_300K_10ps_CENTERED.binpos)
is a BINPOS file with 5000 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> STRIP: 69249 atoms will be removed from trajectory: :761-23843
From the "Processing BINPOS file" message, it seems that
currentCoordinateInfo->type is being correctly set as COORD_BINPOS in
ptraj.c, but this is as far as I've got debugging it.
Any ideas?
As an extended question, how hard would it be to modify the code so that
one could specify a frame parameter to the "reference" command? Hence
one could say, use any frame they wanted from the trajectory:
reference file.binpos 35
regards,
Mark
Received on Wed May 02 2007 - 06:07:22 PDT
