[gmx-users] Reg: fatal error pdb2gmx

[Justin A. Lemkul]

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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