[gmx-users] pdb2gmx-fatal error in output file

[Justin A. Lemkul]

Moeed wrote:
> Hello,
> 
> ****************output.pdb2gmx is giving Fatal error:
> Fatal error:
> Residue '' not found in residue topology database. Do I need to add 
> Hexane topology to rtp file in library?! Please see below. Thank you 
> very much.

It looks like the format of your .pdb file is wrong.  pdb2gmx is finding a chain 
identifier "H" that likely comes from the first letter of "HEX."  The format of 
a .pdb file is very specific, so make sure whatever changes you may have made to 
the file are correct.

-Justin

> 
> ********************************************************************************
> 
> Opening library file ffoplsaa.rtp
> Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
> Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
> Opening library file /chem_soft/gromacs/share/gromacs/top/atommass.dat
> Opening library file /chem_soft/gromacs/share/gromacs/top/vdwradii.dat
> Opening library file /chem_soft/gromacs/share/gromacs/top/dgsolv.dat
> Opening library file /chem_soft/gromacs/share/gromacs/top/electroneg.dat
> Opening library file /chem_soft/gromacs/share/gromacs/top/elements.dat
> Opening library file /chem_soft/gromacs/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.atp
> ^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 
> 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 
> 1^MAtomtype 1^MAtomtype 1^MAtom$
> Opening library file ffoplsaa.rtp
> ^MResidue 1^MResidue 2^MResidue 3^MResidue 4^MResidue 5^MResidue 
> 6^MResidue 7^MResidue 8^MResidue 9^MResidue 10^MResidue 11^MResidue 
> 12^MResidue 13^MResidue 14^MResidue 15^MR$
> Sorting it all out...
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.hdb
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa-n.tdb
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa-c.tdb
> 
> Back Off! I just backed up Hexane-PRODRG.top to ./#Hexane-PRODRG.top.1#
> 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 '' not found in residue topology database
> 
> -------------------------------------------------------
> 
> "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
> 
> WARNING: masses will be determined based on residue and atom names,
>          this can deviate from the real mass of the atom type
> 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
> Entries in vdwradii.dat: 28
> Entries in dgsolv.dat: 7
> Entries in electroneg.dat: 71
> Entries in elements.dat: 218
> Reading Hexane-PRODRG.pdb...
> Read 20 atoms
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 1 residues with 20 atoms
> 
>   chain  #res #atoms
>   1 'H'     1     20
> 
> Reading residue database... (ffoplsaa)
> Processing chain 1 'H' (20 atoms, 1 residues)
> 
> 
> 
> 
> 
> 
> Moeed wrote:
>  > Hello,
>  >
>  > I am trying to generate gro and top file with pdb2gmx program. I have
>  > made a copy of ffoplsaa.rtp from library to working directory and added
>  > Hexane molecule residue to the beginning of the ffoplsaa.rtp.
> 
> <snip>
> 
>  >I type in:
>  >
>  >
>  > pdb2gmx -f Hexane-PRODRG.pdb -o Hexane-PRODRG.gro -p Hexane-PRODRG.top
>  > -ff oplsaa >& output.pdb2gmx
>  >
> 
> In principal, this should work, but if it's not, then stop redirecting your
> output (i.e., let it print to the screen) and see what pdb2gmx is doing.
> Otherwise, inspect this "output.pdb2gmx" for error messages, etc.
> 
> -Justin
> 
>  > I do not get gro file at all and top file I get contains the following
>  > comments only!:
>  >
>  > ;*****************************
> ***************************************
>  > ;       File 'Hexane-PRODRG.top' was generated
>  > ;       By user: moeed (500)
>  > ;       On host: moeed-desktop
>  > ;       At date: Sun May  9 10:47:26 2010
>  > ;
>  > ;       This is your topology file
>  > ;       "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
>  > ;
>  > ; Include forcefield parameters
>  > #include "ffoplsaa.itp"
> 

-- 
========================================

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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