[gmx-users] grompp error

[Mark Abraham]

nitu sharma wrote:
> Dear MARK
> 
>                      Now the problem of matching of topology file and 
> coordinate file solved  but the other two errors come during running 
> grompp in the second step of inflategro .
> my command line is like this- grompp -f em.mdp -p topolinflate.top -c 
> inflated_system.gro -o inflated-em.tpr
> 
> the error came is like this-
> ERROR 1 [file topol_A.itp, line 29912]:
>   No default Proper Dih. types
> 
> 
> ERROR 2 [file topol_B.itp, line 26604]:
>   No default Proper Dih. types

Look at your .itp files. You will see that the proper dihedrals don't 
have functional forms and/or parameters listed on that line. That means 
GROMACS tries to look them up from the ffxxxxbon.itp database for the 
forcefield by matching the atom types of the atoms involved. This error 
means that the forcefield doesn't have such dihedrals. Thus you've made 
some error, such as trying to mix force fields or extending them 
incompletely.

> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 3 bonded neighbours molecule type 'Protein_B'
> Excluding 3 bonded neighbours molecule type 'DMPC'
> 
> NOTE 1 [file topolinflate.top, line 33]:
>   System has non-zero total charge: -1.161999e+01
>  
> 
> 
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> 
> There was 1 note
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.3
> Source code file: grompp.c, line: 986
> 
> Fatal error:
> There were 2 errors in input file(s)
> -------------------------------------------------------
> 
> can you suggest me what is the possible way to solve this problem and in 
> case of note - system has non zero charge how can i make its 
> neutral?????????????????????

One question mark suffices. More makes you sound unprofessional :-)

You have a non-zero charge which is also not an integer. This means your 
topology is broken somehow. Go and look at it. In your [atoms] section 
of a [moleculetype], pdb2gmx will have listed the current total charge 
of the species. This will probably be an integer after the last atom for 
every residue. You will have to detect what's gone wrong, such as 
duplicate termini. Then go and make your topologies properly! Read all 
the options in pdb2gmx -h, if applicable.

Mark