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

[Moeed]

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.

********************************************************************************

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"
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