[gmx-users] DPPC problem

[liu xin]

Hi everyone,

I made a hole in a dppc128 bilayer, after that I merged the bilayer of hole
with the protein manully (just copy and paste), then I want to do a EM with
the merge.pdb.
But when I did pdb2gmx, choosing the 4: GROMOS96 43a2 Forcefield
(development) (improved alkane dihedrals) force field, I got a error told me
that: Residue 'DPP' not found in residue topology database. The output of
pdb2gmx run is below:

Reading merge.pdb...
Read 12520 atoms
Opening library file /home/dong/programs/gromacs_hole/share/top/xlateat.dat
13 out of 13 lines of xlateat.dat converted succesfully
Opening library file
/home/dong/programs/gromacs_hole/share/top/aminoacids.dat
Analyzing pdb file
There are 28 chains and 1 blocks of water and 4104 residues with 12520 atoms

  chain  #res #atoms
  1 'A'     1     50
  2 'B'     1     50
  3 'C'     1     50
  4 'D'     1     50
  5 'E'     1     50
  6 'F'     1     50
  7 'G'     1     50
  8 'H'     1     50
  9 'I'     1     50
  10 'J'     1     50
  11 'K'     1     50
  12 'L'     1     50
  13 'M'     1     50
  14 'N'     1     50
  15 'O'     1     50
  16 'P'     1     50
  17 'Q'     1     50
  18 'R'     1     50
  19 'S'     1     50
  20 'T'     1     50
  21 'U'     1     50
  22 'V'     1     50
  23 'W'     1     50
  24 'X'     1     50
  25 'Y'     1     50
  26 'Z'     1     50
  27 ' '   102   5100
  28 ' '   321   2465
  29 '-'  3655   3655  (only water)

All occupancies are one
Opening library file /home/dong/programs/gromacs_hole/share/top/FF.dat

Select the Force Field:
 0: Gromacs Forcefield (see manual)
 1: Gromacs Forcefield with all hydrogens (proteins only)
 2: GROMOS96 43a1 Forcefield (official distribution)
 3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
 4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4
Using ffG43a2 force field
Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2.atp
Atomtype 47
Reading residue database... (ffG43a2)
Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2.rtp
Using default value - not generating all possible dihedrals
Using default value - excluding 3 bonded neighbors
Residue 95
Sorting it all out...
Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2.hdb
Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2-
n.tdb
Opening library file /home/dong/programs/gromacs_hole/share/top/ffG43a2-
c.tdb
Processing chain 1 'A' (50 atoms, 1 residues)
Opening library file /home/dong/programs/gromacs_hole/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Fatal error: Residue 'DPP' not found in residue topology database

Then, I switched to use the 0: Gromacs Forcefield (see manual), it seemed
that it ran normally except  a warning: 'DPP' not found in residue topology
database, trying to use 'DPPC'. I neglected this warning and continued, but
when I did the "grompp" step, it gave the following messages:

creating statusfile for 1 node...
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1125 of the 1326 non-bonded parameter combinations
WARNING 2 [file "merge_A.itp", line 69]:
  No default Bond types, using zeroes
WARNING 3 [file "merge_A.itp", line 70]:
  No default Bond types, using zeroes
WARNING 4 [file "merge_A.itp", line 71]:
  No default Bond types, using zeroes
WARNING 5 [file "merge_A.itp", line 177]:
  No default Angle types, using zeroes
WARNING 6 [file "merge_A.itp", line 178]:
  No default Angle types, using zeroes
WARNING 7 [file "merge_A.itp", line 179]:
  No default Angle types, using zeroes
WARNING 8 [file "merge_A.itp", line 180]:
  No default Angle types, using zeroes
WARNING 9 [file "merge_A.itp", line 181]:
  No default Angle types, using zeroes
WARNING 10 [file "merge_A.itp", line 182]:
  No default Angle types, using zeroes
Cleaning up temporary file grompp8Crm9R
Fatal error: Too many warnings,
/home/dong/programs/gromacs_hole/i686-pc-linux-gnu/bin/grompp terminated

I think there's some problem in my *.top file, but I don't know how to do
with it, could anybody give me some suggestion?
My dppc128.pdb file is from:
http://moose.bio.ucalgary.ca/index.php?page=Downloads
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