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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