[gmx-users] Reg: fatal error pdb2gmx

[vinothkumar mohanakrishnan]

Hi Justin

I had taken United atom pdb file form PRODRG and i want to use OPLS-UA force
field. i dont know what's wrong out there.I have done it befor for other
molecules like DCE, CCL4 etc.

Regards
Vinoth

On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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