[gmx-users] Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)

[fulya caglar]

Hi Mark,
  I'm so sorry for taking so much of your time.I tried to explain how I generated the sections:
   
  Firstly I  named my ligand (protein) files as  drg  and my protein  files as trp.
   
  Next I generated the drg.itp and trp.top  files with pdb2gmx
   
  pdb2gmx  -ff gmx -f drg.pdb -o drg2 -p drg.top
  pdb2gmx  -ff gmx -f trp.pdb -o trp2.pdb  -p trp.top  -merge -ignh –ss
   
  Then I pasted the coordinates from drg.pdb onto the end of the trp2.file and I edited trp.top file; I added  #include “ drg.itp” and under the [molecules] section my ligand.
   
  I setup the box.
   
  editconf -bt octahedron -f trp2.pdb -o trp2.pdb -c -d 0.8
   
  genbox -cp trp2.pdb  -cs spc216.gro -o trp_b4ion.pdb -p trp.top  
   
   
   
  My em.mdp file 
   title = drg_trp
  cpp = /usr/bin/cpp
  define = -DFLEX_SPC
  constraints = none
  integrator = steep
  dt = 0.002
  nsteps = 500
  nstlist = 10
  ns_type = grid
  rlist = 0.9
  coulombtype = cutoff
  rcoulomb = 0.9
  rvdw = 0.9
  fourierspacing = 0.12
  fourier_nx = 0
  fourier_ny = 0
  fourier_nz = 0
  pme_order = 4
  ewald_rtol = 1e-5
  optimize_fft = yes
  emtol = 1000.0
  emstep = 0.01      
   
  grompp -f em.mdp -c trp_b.pdb -p trp.top -o trp_b.tpr
   After grompp ý got these error.
   ERROR 1 [file "drg.itp", line 7]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 2 [file "drg.itp", line 8]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 3 [file "drg.itp", line 9]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 4 [file "drg.itp", line 10]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 5 [file "drg.itp", line 11]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 6 [file "drg.itp", line 12]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 7 [file "drg.itp", line 13]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 8 [file "drg.itp", line 14]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 9 [file "drg.itp", line 15]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  ERROR 10 [file "drg.itp", line 16]:
    Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
  Cleaning up temporary file gromppWX2Ly6
  -------------------------------------------------------
  Program grompp_mpi, VERSION 3.3.1
  Source code file: fatal.c, line: 416
   
  Fatal error:
  Too many warnings, grompp_mpi terminated
  -------------------------------------------------------
  Fulya

Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
  fulya caglar wrote:
> Hi Mark,
> I checked my .top file and I saw that there is no q0 column under the 
> [dihedrals] in the complex topology file but there is q0 column in the 
> ligand protein .top file.Dou you think that it is the source of my 
> problem?Thanks very much.

I don't know... you'll have to give examples and explain *fully* how you 
generated the sections.

Mark
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