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

[David]

On Mon, 2003-06-09 at 18:58, Minghu Song wrote:
> 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"
chek all itp files. Only one should include ffgmx.itp
if your protein itp comes from pdb2gmx you probably have another one
there. 
> 
> 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+? )
You have some options:
1. leave the loops in
2. replace the lopps by shorter ones (e.g. 3-4 Gly or Ala residues)
3. use separate protein chains

If you cut out the loops with doing anything, gromacs will think there
is a bond between the ends of loop (this is your warning) and hence will
try to move together these ends with destructive consequences.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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