shahrbanoo karbalaee wrote:
hi justin
I have a file tfe peptide water,cl .I minimized it and I want to
preequilbrate it.when I do the grompp I get 1 warning:
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for TFE 200
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 913
turning all bonds into constraints...
Excluding 1 bonded neighbours for CL- 1
turning all bonds into constraints...
NOTE:
System has non-zero total charge: -1.000003e+00
Perhaps you want another chloride ion?
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
Reading position restraint coords from emout.gro
renumbering atomtypes...
converting bonded parameters...
# G96ANGLES: 1803
# PDIHS: 468
# IDIHS: 68
# LJ14: 1010
# POSRES: 105
# CONSTR: 1339
# SETTLE: 913
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are: 1114 OTHER residues
There are: 14 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 (138 out of
4278)
Maybe you want to try Protein and Non-Protein instead?
; Berendsen temperature coupling is on
Tcoupl = berendsen
pcoupltype = isotropic
tau_t = 0.1 0.1
tc-grps = Protein non-protein
ref_t = 300 300
I think this is probably an issue with case-sensitivity. The warning
exists to help people avoid erroneously coupling a handful of ions to
their own thermostat. Your system is probably fine with the two kinds of
groups you have. You could just ignore the warning, or edit your .mdp
file (and/or index file) to capitalize to "Non-Protein"
Mark
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