[gmx-users] Added Residue Name [ HFL ] in ffgmx.rtp, still have err message says

[Feng Xu]

Fatal error:
Residue 'HFL' not found in residue topology database

the portion of ffgmax.rtp file relevant is:

.....
[ HFL ]
   [ atoms ]
     HHF   HHF   0.725     0
     FHF   FHF   0.725     0

[ HIS1 ]
.......

Atom types HHF and FHF are also defined in relevant .atp file.

and a simple HF.pdb file is :

 ATOM      1  HHF HFL     1       0.000   0.000   0.000  1.00  0.00
 ATOM      2  FHF  HFL     1       0.091   0.000   0.000  1.00  0.00
 ATOM      3  HHF HFL     2       0.291   0.000   0.000  1.00  0.00
 ATOM      4  FHF  HFL     2       0.291   0.091   0.000  1.00  0.00


after issue command "pdb2gmx -f HF.pdb", the following output is produced:

.......Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.rtp
Opening library file /home/fxu/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /home/fxu/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file /home/fxu/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
         this can deviate from the real mass of the atom type
Opening library file /home/fxu/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /home/fxu/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /home/fxu/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /home/fxu/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading HF.pdb...
Read 'Liquid HydroFloride  - Yummie!', 4 atoms
Opening library file /home/fxu/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 2 residues with 4 atoms

  chain  #res #atoms
  1 ' '     2      4

All occupancies are one
Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.atp
Atomtype 1
Reading residue database... (ffgmx)
Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.rtp
Residue 98
Sorting it all out...
Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx.hdb
Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx-n.tdb
Opening library file /home/fxu/gromacs/share/gromacs/top/ffgmx-c.tdb

Back Off! I just backed up topol.top to ./#topol.top.11#
Processing chain 1 (4 atoms, 2 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds

-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.7
Source code file: resall.c, line: 426

Fatal error:
Residue 'HFL' not found in residue topology database

-------------------------------------------------------

"If You See Me Getting High, Knock Me Down" (Red Hot Chili Peppers)


What is wrong here?

Thanks,

Feng Xu

Postdoc  @ Iowa State University
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