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

[Justin A. Lemkul]

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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