[gmx-users] grompp error

nitu sharma sharmanitu35 at gmail.com
Fri Apr 24 06:40:27 CEST 2009


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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