[gmx-users] Grompp Error message: Found a second defaults directive, file "ffgmx.itp", line 6

Minghu Song songm at rpi.edu
Mon Jun 9 19:00:01 CEST 2003

Hello, Dear gmx-users,

I tried to generate the *.tpr for the system with a  membrane protein 
(mainly  helix core)embeded in the lipid bilayer, which had been obtained
by making hole in the lipid bilayer ( Thanks Dr. Smith)  and then merged 
the protein and lipid bilayer into  a new file -- mempro_lipid.pdb.     

The following was what I tried to generate the *.tpr: ( I kept an extra 
copy of the correponding *.itp in current directory)
pdb2gmx -f mempro.pdb -o mempro.pdb_wh.gro -p mempro_wh.top  ( with 
gromacs force field, option 0)
mv mempro_wh.top  mempro_wh.itp and then delete the sentence after the 
line "; Include Position restraint file " for itp file
editconf -f pdb_wh.gro -o  pdb_wh.pdb
manually modified the mempro_lipid.pdb file for the part related with 
mempro.pdb (from 'without hydrogen' to 'including hydrogen')
then edited the mempro_lipid.top
#include "ffgmx.itp"
#include "mempro_wh.itp"
#include "dppc.itp"
[ molecules ]
; name    number
Protein 1
DPPC    109
SOL     5504 

grompp -f em.mdp -o b4em.tpr -c mempro_lipid.pdb -r mempro_lipid.pdb -p 
mempro_lipid. top

I got the following error message :
calling /lib/cpp...
processing topology...
Cleaning up temporary file gromppFLTSYF
Fatal error: Found a second defaults directive, file "ffgmx.itp", line 6"

In my case, the membrane protein was obtained by homology modeling. In 
the previous preprocess step (before doing any MD inlcuding making hole 
process),  I deleted three long loop sections and just kept the helix 
core for the mempro.pdb,which cause the warning of three long bond 
(>1.2nm) during pdb2gmx step.   Is it the problem that leads to the 
above error message?  Should I delete the bond and angle information of 
those incorrected "connection" from the correponding itp file?  Or 
should I prepare several *itp files such as helixI.itp , helixII.itp ... 
, instead of just using one membrepro.itp and then add them into top 
file? If so, how to deal with the termial residues of those helix (in 
cytoplasmic/extracellular sides)? (using COO- and NH3+? )

Can someone give me some suggestion how to fix the above problemd? 
Thanks in advance!

Minghu Song

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