[gmx-users] Reg: fatal error pdb2gmx

vinothkumar mohanakrishnan kmvinoth at gmail.com
Mon Dec 20 07:00:57 CET 2010 

Even though the UA force field is outdated i want to use that and try to
rectify the cryptic error message that keeps coming. Thank you very much for
your suggestions Justin.

Regards
Vinoth

On Mon, Dec 20, 2010 at 11:15 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
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