[gmx-users] WARNING 1 [file aminoacids.dat, line 1]

[Chih-Ying Lin]

Hi
I used the command.
grompp -f fullmd.mdp -c minimized_water.gro -p xxx.top -o fullmd.tpr
It showed the following WARNING.
WARNING 1 [file aminoacids.dat, line 1]

My system did not include any protein.
So, could I skip/neglect the WARNING??

Thank you
Lin




The following is the message after send the above command.
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
calling /usr/libexec/gcc/darwin/ppc/3.3/cpp...
processing topology...
Generated 141 of the 1176 non-bonded parameter combinations
Excluding 3 bonded neighbours for azoct 1
Excluding 2 bonded neighbours for SOL 1209
NOTE:
  System has non-zero total charge: 1.000000e+00

processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   34
#  G96ANGLES:   50
#      PDIHS:   64
#      IDIHS:   12
#       LJ14:   11
#     SETTLE:   1209
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are:  1210      OTHER residues
There are:     0    PROTEIN residues
There are:     0        DNA residues
Analysing Other...
WARNING 1 [file aminoacids.dat, line 1]:
  T-Coupling group azoct has fewer than 10% of the atoms (33 out of 3660)
  Maybe you want to try Protein and Non-Protein instead?
Making dummy/rest group for Acceleration containing 3660 elements
Making dummy/rest group for Freeze containing 3660 elements
Making dummy/rest group for VCM containing 3660 elements
Number of degrees of freedom in T-Coupling group azoct is 98.96
Number of degrees of freedom in T-Coupling group SOL is 7251.04
Making dummy/rest group for User1 containing 3660 elements
Making dummy/rest group for User2 containing 3660 elements
Making dummy/rest group for Or. Res. Fit containing 3660 elements
Making dummy/rest group for QMMM containing 3660 elements
T-Coupling       has 2 element(s): azoct SOL
Energy Mon.      has 2 element(s): azoct SOL
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): azoct
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 fullmd.tpr to ./#fullmd.tpr.1#

There was 1 warning

gcq#293: "There's Still Time to Change the Rope You're On" (Led Zeppelin)