On 1/6/10 5:05 PM, Feng Xu wrote:
Fatal error:
Residue'HFL' not found in residue topology database
the portion of ffgmax.rtp file relevant is:
If you have a file called "ffgmax.rtp", then none of the changes you made are
going to be applied, since pdb2gmx is expecting ffgmx* files. The reason I say
this is because your example works quite perfectly for me using the .rtp entry
and .pdb file you've posted.
.....
[ HFL ]
[ atoms ]
HHF HHF 0.725 0
FHF FHF 0.725 0
Some unsolicited advice: surely you want a negative charge on the fluorine, and
a bond between these two atoms, correct?
[ 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
Maybe there is an issue with spacing? PDB format is fixed, and the spacing
between your atom names and residue names is not correct on all lines (assuming
this is not just some weird behavior of my email client, but it does appear
incorrect using a fixed-format font.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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