[gmx-users] Reg: fatal error pdb2gmx
Justin A. Lemkul
jalemkul at vt.edu
Mon Dec 20 06:45:18 CET 2010
vinothkumar mohanakrishnan wrote:
> Hi Justin
>
> I had taken United atom pdb file form PRODRG and i want to use OPLS-UA
Interesting choice. That's an antiquated force field...
> force field. i dont know what's wrong out there.I have done it befor for
> other molecules like DCE, CCL4 etc.
>
To create a topology for a simple six-atom molecule, pdb2gmx is unnecessary.
Just write the topology by hand. You've effectively already done so. Or, you
can try to troubleshoot an unfortunately cryptic error message.
-Justin
> Regards
> Vinoth
>
> On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> vinothkumar mohanakrishnan wrote:
>
> Hi all
>
> I want to use pdb2gmx to generate hexane topology and hexane.gro
> file. i have added the atom name in .atp file and corresponding
> section in .rtp file. i have given below my .rtp entry
>
> [ DRG ]
> [ atoms ]
> CAA opls_966 0 1
> CAF opls_966 0 1
> CAB opls_967 0 2
> CAC opls_967 0 2
> CAD opls_967 0 2
> CAE opls_967 0 2
> [ bonds ]
> CAA CAB
> CAB CAC
> CAC CAD
> CAD CAE
> CAE CAF
> [ angles ]
> CAA CAB CAC
> CAB CAC CAD
> CAC CAD CAE
> CAD CAE CAF
> [ dihedrals ]
> CAA CAB CAC CAD
> CAB CAC CAD CAE
> CAC CAD CAE CAF
>
> but i get the error message as given below and it doesn't
> generate any .top and .gro file . I searched the mailing list
> and found a similar post but there is no solution
> (http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html)
> previously i used pdb2gmx for other molecules and it worked fine
> for the oplsaa force field. any help is highly appreciated.
>
> Opening library file ffoplsaa.rtp
> Opening library file
> /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Opening library file
> /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> WARNING: masses will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
> Opening library file
> /usr/local/gromacs/share/gromacs/top/atommass.dat
> 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
> Opening library file vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file
> /usr/local/gromacs/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file
> /usr/local/gromacs/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading hexane.pdb...
> Read 6 atoms
> Opening library file
> /usr/local/gromacs/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
>
> chain #res #atoms
> 1 ' ' 1 6
> All occupancies are one
> Opening library file ffoplsaa.atp
> Atomtype 1
> Reading residue database... (ffoplsaa)
> Opening library file ffoplsaa.rtp
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.7
> Source code file: resall.c, line: 279
>
> Fatal error:
> in .rtp file at line:
>
>
> -------------------------------------------------------
>
>
> There is something wrong with the format of your .rtp file.
> Unfortunately, the error message in this case is not particularly
> helpful.
>
> Based on the residue and atom naming, it appears that you're trying
> to interface some sort of PRODRG output with OPLS-AA. Doing so is
> fundamentally flawed, mostly because PRODRG gives GROMOS-compatible
> topologies (often poor ones, at that). Presumably, you have
> introduced new atom types (opls_966/967) corresponding to some
> united-atom C type. OPLS-AA is an all-atom force field, so
> introducing a united-atom hexane topology is simply wrong, unless
> you have somehow demonstrated that a united-atom model behaves
> properly and you have done the thorough work of parameterizing this
> model.
>
> -Justin
>
> Regards
> Vinoth
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
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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