[gmx-users] genion error

[Hiromichi Tsurui]

Thank you,David;

As you suggeted,I ran genion with the options and got confout.gro.
I then edited 2IAD_corr_ABP.top file, removing 14 solvent molecules and
adding 14 NA+ ions. 
Then I ran grompp;
grompp -f equ-l0.00.mdp -p ../../2IAD_corr_ABP.top -c
../../EQ2/confout.gro 

and response was as follows;

checking input for internal ocnsistency...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_P 1
Excluding 3 bonded neighbours for Protein_B 1
Excluding 2 bonded neighbours for SOL 29553
Excluding 1 bonded neighbours for NA+ 14
WARNING 1 [file "../../2IAD_corr_ABP.top", line 41]:
  State B has non-zero total charge: 8.500036e-01

Processing coordinates...
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
Warning: atom names in ../../2IAD_corr_ABP.top and ../../EQ2/confout.gro
don't match (NA - Na)
WARNING 2 [file "../../2IAD_corr_ABP.top", line 41]
  14 non-matching atom names
  atom names from ../../2IAD_corr_ABP.top will be used
  atom names from ../../EQ2/confout.gro will be ignored

double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
Waking down the molecules graph to make shake-blocks
initialising group options...
processing index file...
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Making dummy/rest group for T-Coupling containing 14 elements
Fatal error: Not enoughref_t and tau_t values!



I am trying to estimate binding energy of peptide P and protein (A+B) by
thermodynamic integration. In B state, all the atoms in peptide P is
replace with dummy atoms. This calculation was at the stage after 100000
steps of equiblation, and just begining of the simmulation at lambda 0,
for 25000 steps of equiblation. The mdp file for this culclation is as
follows;

cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
tinit               =  0.0
dt                  =  0.002    
nsteps              =  25000      
nstcomm             =  1
nstxout             =  1000
nstvout             =  0
nstfout             =  0
nstlog              =  500
nstenergy           =  250
nstxtcout           =  1000
xtc_precision       =  1000
xtc_grps            =  Protein 
nstlist             =  5
energygrps          =  Protein SOL
ns_type             =  grid
rlist               =  0.9
coulombtype         =  Reaction-Field
epsilon_r           =  78.0
rcoulomb            =  1.4
rvdw                =  1.4
Tcoupl              =  Berendsen
tc-grps             =  Protein SOL
ref_t               =  300 300
tau_t               =  0.1 0.1
Pcoupl              =  Berendsen
tau_p               =  1.0
compressibility     =  4.6e-5
ref_p               =  1.0
free_energy         =  yes
init_lambda         =  0.00
sc-alpha            =  1.51


Please let me know what values of ref_t and tau_t is appropriate for
this calculation. And any other points to correct.

Thank you.








2006/01/15 (æ—¥) 20:44  David van der Spoel wrote:
> Hiromichi Tsurui wrote:
> > Dear Gromax users;
> >
> >
> > I want to neutralize my system consisting of a protein and spc water
> > molecules. After I determined the charge to neutralize using grompp (the
> > system has -14), I entered as follows;
> >
> > genion -s topol.tpr -c confout.gro -np 14
> > then appeared 
> >
> >
> > Select a continuous group of solvent molecule
> >
> > Opening a library file /usr/local/gromacs/share/top/aminoacids.dat
> >
> > Group 0 ( System) has 92736 elements
> >
> > Group 1 ( Protein) has 4035 elements
> >
> > Group 2 ( Protein-H) has 3144 elements
> >
> > .
> >
> > .
> >
> > .
> >
> > .
> >
> > .
> >
> > Group 13 ( Other ) has 88701 elements
> >
> > Select a group:
> >
> >
> > However, after I entered 0, error message appeared,
> >
> >
> > Fatal error : Your solvent group size (92736) is not a multiple of 11
> >
> >
> > When I entered 1,
> >
> > Fatal error : Your solvent group size (4035) is not a multiple of 11
> >
> >
> > When I entered 2,
> >
> > Fatal error : The solvent group is not continuous: index[1]=1,
> > index[2]=5
> >
> >
> > When I entered 3,
> >
> > Fatal error : The solvent group is not continuous: index[1]=5,
> > index[2]=14
> >
> >
> > When I entered 4,
> >
> > Fatal error : The solvent group is not continuous: index[1]=1,
> > index[2]=5
> >
> >
> > and so on.
> >
> > How shold I neutralize the system ?
> >   
> 
> select solvent group.
> 
> use -random option as well.
> >
> > Thank you for your cooperation.
> >
> >
> >
> >
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