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
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?????????????????????
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