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

[Yang Ye]

Hi, It is not the problem of your command line. It is related to how index file is used with grompp. In general, there are pre-defined groups - protein, non-protein, protein-H, etc; and there are user-defined groups. In your case, Protein1 and TOYPEP are both user-defined groups. So did you miss anything in the tutorial/example? Read the manual more carefully to understand how grompp works. This list just tries to help any user but not spoon-feed. Regards, Yang Ye On 10/24/08 3:19 PM, wang wrote: 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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