wara boon wrote:
Hello,
I pull molecule into membrane by MD simulations but it error about
processing topology...
Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmx.itp
Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxnb.itp
Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxbon.itp
Opening library file /home/Ell/gromacMPI/share/gromacs/top/ff_dum.itp
Generated 1284 of the 1485 non-bonded parameter combinations
Opening library file /home/Ell/gromacMPI/share/gromacs/top/spc.itp
Opening library file /home/Ell/gromacMPI/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_C'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_D'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_E'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_F'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_G'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_H'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_I'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_J'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_K'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_L'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_M'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_N'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_O'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_P'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_Q'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_R'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_S'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_T'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_U'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_V'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_W'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_X'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_Y'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_Z'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'VIV'
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 325 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /home/Ell/gromacMPI/share/gromacs/top/aminoacids.dat
There are: 3784 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
Pull group 0 'DPP' has 6400 atoms
Pull group 1 'VIV' has 32 atoms
Making dummy/rest group for Acceleration containing 17397 elements
Making dummy/rest group for Freeze containing 17397 elements
Making dummy/rest group for Energy Mon. containing 17397 elements
Making dummy/rest group for VCM containing 17397 elements
Number of degrees of freedom in T-Coupling group DPP is 12926.89
Number of degrees of freedom in T-Coupling group VIV is 62.99
Number of degrees of freedom in T-Coupling group SOL is 21928.12
Making dummy/rest group for User1 containing 17397 elements
Making dummy/rest group for User2 containing 17397 elements
Making dummy/rest group for XTC containing 17397 elements
Making dummy/rest group for Or. Res. Fit containing 17397 elements
Making dummy/rest group for QMMM containing 17397 elements
T-Coupling has 3 element(s): DPP VIV SOL
Energy Mon. has 1 element(s): 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...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 13x13x14, spacing 0.490 0.492 0.477
Pull group natoms pbc atom distance at start reference at t=0
0 6400 3200
1 32 17381 2.401 -99999.422
Estimate for the relative computational load of the PME mesh part: 0.49
This run will generate roughly 3 Mb of data
writing run input file...
There was 1 warning
-------------------------------------------------------
Program grompp_mpi, VERSION 4.0.2
Source code file: gmx_fatal.c, line: 481
Fatal error:
Too many warnings (1), grompp_mpi terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
-------------------------------------------------------
There's no warning given in the partial output text you've supplied, so
we can't help you diagnose. Also, you should update from 4.0.2, which is
at least 6 months out of date.
Mark
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