[gmx-users] Topology file-residue unknown

Mark Abraham mark.j.abraham at gmail.com
Sat Apr 6 11:00:49 CEST 2013 

On Sat, Apr 6, 2013 at 5:56 AM, Juliette N. <joojoojooon at gmail.com> wrote:

> Thank you Justin. I have now the topology. I have a quick question
> regarding atom types. I used opls_143 and opls_144 for C and H of ethylene
> respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe
> these are not the proper atomtypes for H2C=CH2.
>

http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds

Mark


>
> rtp entry:
>
> [ 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
>
> >From atomtypes.atp
>
> opls_141   12.01100  ; alkene C (R2-C=)
>  opls_142   12.01100  ; alkene C (RH-C=)
> * opls_143   12.01100  ; alkene C (H2-C=)
>  opls_144    1.00800  ; alkene H (H-C=)*
>
> Did I select the correct atomtypes?
> Thanks many times!
>
>
>
>
> On 4 April 2013 18:23, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > 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<
> 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
> >
> > --
> > ==============================**==========
> >
> > 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<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==============================**==========
> > --
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>
> --
> Thanks,
> J. N.
> --
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