[gmx-users] T-Coupling group Protein has fewer than 10% of the atoms

[akalabya bissoyi]

hello everybody
i am trying to setup the position restrained dynamics
 but failed to proceed,-

in  terminal window it shows the massage-

calling /usr/bin/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for UNK 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 44524
turning all bonds into constraints...
Excluding 1 bonded neighbours for Cl 16
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
Reading position restraint coords from god_b4em.pdb
renumbering atomtypes...
converting bonded parameters...
#     ANGLES:   6075
#      PDIHS:   2098
#      IDIHS:   2246
#       LJ14:   7545
#     POSRES:   3088
#     CONSTR:   4142
#     SETTLE:   44524
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/share/gromacs/top/aminoacids.dat
There are: 44541      OTHER residues
There are:   396    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...
WARNING 1 [file aminoacids.dat, line 1]:
  T-Coupling group Protein has fewer than 10% of the atoms (4007 out of
  137634)
  Maybe you want to try Protein and Non-Protein instead?
Making dummy/rest group for Acceleration containing 137634 elements
Making dummy/rest group for Freeze containing 137634 elements
Making dummy/rest group for Energy Mon. containing 55 elements
Making dummy/rest group for VCM containing 137634 elements
Number of degrees of freedom in T-Coupling group Protein is 7921.91
Number of degrees of freedom in T-Coupling group Non-Protein is 267263.09
Making dummy/rest group for User1 containing 137634 elements
Making dummy/rest group for User2 containing 137634 elements
Making dummy/rest group for XTC containing 137634 elements
Making dummy/rest group for Or. Res. Fit containing 137634 elements
Making dummy/rest group for QMMM containing 137634 elements
T-Coupling       has 2 element(s): Protein Non-Protein
Energy Mon.      has 3 element(s): Protein SOL rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...
writing run input file...

Back Off! I just backed up pr.tpr to ./#pr.tpr.2#

There was 1 warning

gcq#194: "You Crashed Into the Swamps" (Silicon Graphics)

root at bioinfo-desktop:/usr/local/gromacs/god2# nohup mdrun -deffnm pr &
[1] 6846
nohup: ignoring input and appending output to `nohup.out'


any body can recognize the error,i am attaching the pr.mdp file.

Thank you have nice day.

 AKALABYA BISSOYI
NIT ROURKELA,INDIA
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