[gmx-users] About the example case "A toy peptide in water" and other protein case (CG martini force field )

[wang]

Dear Sir ,
I used your CG parameters and gromacs V3.3 to simulate protein
aggregation. And my command is :
grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp
The error message is :
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
# BONDS: 1935
# G96ANGLES: 2565
# IDIHS: 225
# CONSTR: 900
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat
There are: 76048 OTHER residues
There are: 1170 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...

-------------------------------------------------------
Program grompp_mpi_d, VERSION 3.3.3
Source code file: readir.c, line: 798

Fatal error:
Group Protein1 not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option.

But I tried your example case "A toy peptide in water" , I still got the
same error .
My command is :

1.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c
toypeptide.gro -n index.ndx -o toypeptide.tpr

2.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c
toypeptide.gro -o toypeptide.tpr

____________________________________________________________________________________
index.ndx :

[ prot_sort ]

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

16 17 18 19 20

--------------------------------------------------------------------------------------------------------------------------------------------------------
The error message :

Walking down the molecule graph to make shake-blocks

initialising group options...

processing index file...

-------------------------------------------------------

Program grompp_mpi_d, VERSION 3.3.3

Source code file: readir.c, line: 798

Fatal error:

Group TOYPEP not found in indexfile.

Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.

In that case use the '-n' option.



Sir, could you tell me how to fix the problem? By the way, I test other
cases in your website and I didn't get any error message .
Best regards

Wang Yeng-tseng
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