[gmx-users] Grompp Error message: Found a second defaults directive, file "ffgmx.itp", line 6
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
[ molecules ]
; name number
grompp -f em.mdp -o b4em.tpr -c mempro_lipid.pdb -r mempro_lipid.pdb -p
I got the following error message :
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!
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