[gmx-users] tpbconv error with 3.3_beta_20050202

[Dallas B. Warren]

Bess,

> Explicitly setting the -f option will solve the problem.
> I the latest CVS I had already implemented that tpbconv will 
> not do the subgroup stuff when -f, -time, -extend or -until is set.

The command line that I use to call it is as follows:

	tpbconv -s md_69.tpr -f md_69.trr -e md_69.edr -o md_70.tpr
-extend 4000

The output that comes out is as follows:

###########################################################

Option     Filename  Type         Description
------------------------------------------------------------
  -s      md_69.tpr  Input        Generic run input: tpr tpb tpa xml
  -f      md_69.trr  Input, Opt!  Full precision trajectory: trr trj
  -e      md_69.edr  Input, Opt!  Generic energy: edr ene
  -n      index.ndx  Input, Opt.  Index file
  -o      md_70.tpr  Output       Generic run input: tpr tpb tpa xml

      Option   Type  Value  Description
------------------------------------------------------
      -[no]h   bool     no  Print help info and quit
       -nice    int      0  Set the nicelevel
       -time   real     -1  Continue from frame at this time (ps)
instead of
                            the last frame
     -extend   real    400  Extend runtime by this amount (ps)
      -until   real      0  Extend runtime until this ending time (ps)
  -[no]zeroq   bool     no  Set the charges of a group (from the index)
to
                            zero
-[no]unconstrained
               bool    yes  For a continuous trajectory, the constraints
                            should not be solved before the first step
                            (default)

Reading toplogy and shit from md_69.tpr
Reading file md_69.tpr, VERSION 3.3_beta_20050202 (single precision)
Modifying ir->bUncStart to TRUE

READING COORDS, VELS AND BOX FROM TRAJECTORY md_69.trr...

trn version: GMX_trn_file (single precision)

Read frame      0: step      0 time    0.000
Read frame      1: step  20000 time  100.000
Read frame      2: step  20000 time  100.000

Using frame of step 20000 time 100
Opened md_69.edr as single precision energy file

Reading frame      0 time    0.000           
Reading frame      1 time    2.000           
Reading frame      2 time    4.000           
Reading frame      3 time    6.000           
Reading frame      4 time    8.000           
Reading frame      5 time   10.000           
Reading frame      6 time   12.000           
Reading frame      7 time   14.000           
Reading frame      8 time   16.000           
Reading frame      9 time   18.000           
Reading frame     10 time   20.000           
Reading frame     20 time   40.000           
Reading frame     30 time   60.000           
Reading frame     40 time   80.000           
Reading frame     50 time  100.000           

READ 3 PRESSURE COUPLING MU'S FROM md_69.edr

Opening library file /opt/gromacs-3.3b1/share/top/aminoacids.dat
Group     0 (      System) has 509856 elements
Group     1 (         DGL) has 158400 elements
Group     2 (         MGL) has 100800 elements
Group     3 (         SOL) has 250656 elements
Select a group: -------------------------------------------------------
Program tpbconv, VERSION 3.3_beta_20050202
Source code file: index.c, line: 657

Fatal error:
Cannot read from input
-------------------------------------------------------

"Got Coffee, Got Donuts, Got Wasted" (F. Black)

###########################################################

To reiterate, this worked fine with 3.2.1.  I don't use the -n
option/switch.  And even if I do include it on the command line,
containing a single group consisting of the entire system, the fatal
error still occurs.

Should I see about getting the guys to updated to the latest CVS
version? i.e. some bug that appeared and may have been fixed?

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.