[gmx-users] Topology file-residue unknown

[Justin Lemkul]

On 4/4/13 6:17 PM, Juliette N. wrote:
> Hi Justin,
>
> Thanks a lot for your message. I am petrified why pdb2gmx is not
> recognizing the residue ETY. This the first residue added to ffoplsaa.rtp
> but as you may see below it is not read from rtp.
>
> I am sure this residue is added to ffoplsaa.rtp which is existing in the
> working directory:
>
> [ ETY ]
>   [ atoms ]
>     C1    opls_143    -0.120    1
>     H11   opls_144     0.060    1
>     H12   opls_144     0.060    1
>     C2    opls_143    -0.120    2
>     H21   opls_144     0.060    2
>     H22   opls_144     0.060    2
>
> [ bonds ]
>     C1    H11
>     C1    H12
>     C1    C2
>     C2    H21
>     C2    H22
>    ;C2    C1
>
> Then I issue:
>
> pdb2gmx -f Ethylene.gro -o GRO.gro -p Ethylene.top -ff oplsaa
>                           :-)  G  R  O  M  A  C  S  (-:
>
>                        GROwing Monsters And Cloning Shrimps
>
>                              :-)  VERSION 4.5.4  (-:
>
> Using the Oplsaa force field in directory oplsaa.ff
>
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat
>
> Select the Water Model:
>   1: TIP4P  TIP 4-point, recommended
>   2: TIP3P  TIP 3-point
>   3: TIP5P  TIP 5-point
>   4: SPC    simple point charge
>   5: SPC/E  extended simple point charge
>   6: None
> 6
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
> Reading Ethylene.gro...
> Read 'Giant Rising Ordinary Mutants for A Clerical Setup', 6 atoms
> Analyzing pdb file
> Splitting PDB chains based on TER records or changing chain id.
> There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
>
>    chain  #res #atoms
>    1 ' '     1      6
>
> No occupancies in Ethylene.gro
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (oplsaa)
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
> Residue 56
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
>
> Back Off! I just backed up Ethylene.top to ./#Ethylene.top.1#
> Processing chain 1 (6 atoms, 1 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Warning: Starting residue ETY1 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: resall.c, line: 581
>
> Fatal error:
> Residue 'ETY' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> I am kind of baffled what could be wrong. I would really appreciate if you
> could comment on this. Is there a bug in pdb2gmx version 4.5.4 (which I
> doubt)?
> Do i have to edit esiduetypes.dat?
>

You've added the .rtp entry incorrectly.  pdb2gmx in version 4.5 and above needs 
.rtp files to be organized in force field subdirectories (in your case 
oplsaa.ff).  It will not recognize a file called "ffoplsaa.rtp," which is the 
pre-4.5 syntax for force field files.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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