[gmx-users] what's wrong with rtp file?

nanyu101 at sina.com nanyu101 at sina.com
Tue Jun 8 12:54:13 CEST 2004

Dear gmx-users,

   I have met some problems in running pdb2gmx_d command..the information given by computer was listed as following. Who can tell me what happened in my operations?

Reading test.pdb...
Read 'pptemp.pdb', 259 atoms
Opening library file /usr/local/gromacs/share/top/xlateat.dat
13 out of 13 lines of xlateat.dat converted succesfully
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Analyzing pdb file
There are 2 chains and 0 blocks of water and 7 residues with 259 atoms

  chain  #res #atoms
  1 '1'     1      6  
  2 '2'     7    253  

WARNING: there were 8 atoms with zero occupancy and 251 atoms with
         occupancy unequal to one (out of 259 atoms). Check your pdb file.
Opening library file /usr/local/gromacs/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)
Using ffG43a2 force field
Opening library file /usr/local/gromacs/share/top/ffG43a2.atp
Atomtype 47
Reading residue database... (ffG43a2)
Opening library file ffG43a2.rtp
Using default value - not generating all possible dihedrals
Using default value - excluding 3 bonded neighbors
Residue 3Fatal error: in .rtp file in residue PPI at line:
    H1   H    0.51

Best wishes,

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