[gmx-users] problems in setup the protein+ membrane

chiloo777 777 chiloo777 at gmail.com
Fri Feb 12 02:16:42 CET 2010

Dear all,

I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"

-Before this process, i've changed the ffG53a6nb.itp & ff53Ga6bon.itp
according to the tutorial

my topology, you can see the attached files.
Thanks in advance

Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations

ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
  No default Proper Dih. types

Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947

Fatal error:
Atomtype HO not found

"There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)

Other mails:
chiloo7 at hotmail.com
chiloo77 at yahoo.com
lchitt at kku.ac.th

More information about the gromacs.org_gmx-users mailing list