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

David spoel at xray.bmc.uu.se
Mon Jun 9 19:10:01 CEST 2003

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
> 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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