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

[Mark Abraham]

On 10/05/2010 1:49 AM, Justin A. Lemkul wrote:
>
>
> 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.

... and if you want pdb2gmx to produce a hexane topology, then yes, you 
need an .rtp entry. This is almost as much work as producing a hexane 
topology by hand.

Mark

>> ********************************************************************************
>>
>>
>> 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"
>>
>