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
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