[gmx-users] Error by pdb2gmx

[Yanmei Song]

Dear Mark:

This error is being provoked at the top of the .rtp file when a line with
something like "[header]" is not parsing suitably. A while ago I suggested
using diff on the .rtp file. Do that.


Would you mind telling me how to do that in detail?

I tried the following and it doesn't work.

diff
[ PDM ]
; designation arbitrary, C1 and C2 is -CH3
  [ atoms ]
   SI1   SI           0.300    1
    C1   opls_069     0.000    1
    C2   opls_069     0.000    1
    O1   opls_108    -0.300    1

 [ bonds ]
   SI1   -O1
   SI1   C1
   SI1   C2
   SI1   O1
    O1   +SI1


; Terminal PDMS residue ("beginning" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDMB ]
 [ atoms ]
   C1    opls_069     0.000    1
  SI1    SI           0.300    1
   C2    opls_069     0.000    1
   C3    opls_069     0.000    1
   O1    opls_108    -0.300    1

 [ bonds ]
   SI1   C1
   SI1   C2
   SI1   C3
   SI1   O1
    O1   +SI1


; Terminal PE residue ("end" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3

[ PDME ]
 [ atoms ]
   SI1    SI          0.000    1
   C1    opls_069     0.000    1
   C2    opls_069     0.000    1
   C3    opls_069     0.000    1

 [ bonds ]
   SI1   -O1
   SI1   C1
   SI1   C2
   SI1   C3
diff



Thanks a lot in advance!


On Mon, May 4, 2009 at 10:15 PM, Mark Abraham <Mark.Abraham at anu.edu.au>
wrote:
> Justin A. Lemkul wrote:
>>
>> Then it seems clear to me that your installation of Gromacs is faulty.
>>  Have you tried running the test set (available on the wiki site)?  If
you
>> can describe your computer system (OS, version, compilers used,
>> configuration options, etc.) then perhaps someone on the list can spot a
>> potential pitfall.
>>
>> -Justin
>>
>> Yanmei Song wrote:
>>>
>>> Dear Justin:
>>>
>>> Thank you so much for your help earlier. I updated my GROMACS to
>>> 4.0.4. When I run pdb2gmx using the following two files. I still got
>>> the similar error message:
>>>
>>> Opening library file ffoplsaa.rtp
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
>>> Opening library file
>>> /packages/gromacs-4.0.4/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
>>> /packages/gromacs-4.0.4/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
>>> /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
>>> Entries in vdwradii.dat: 28
>>> Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
>>> Entries in dgsolv.dat: 7
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
>>> Entries in electroneg.dat: 71
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
>>> Entries in elements.dat: 218
>>> Reading pdms2.pdb...
>>> Read 13 atoms
>>> Opening library file
>>> /packages/gromacs-4.0.4/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 3 residues with 13 atoms
>>>
>>>  chain  #res #atoms
>>>  1 ' '     3     13
>>>
>>> All occupancies are one
>>> Opening library file
>>> /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
>>> Atomtype 1
>>> Reading residue database... (ffoplsaa)
>>> Opening library file ffoplsaa.rtp
>>>
>>> -------------------------------------------------------
>>> Program pdb2gmx_d, VERSION 4.0.4
>>> Source code file: resall.c, line: 279
>>>
>>> Fatal error:
>>> in .rtp file at line:
>>>
>>>
>>> -------------------------------------------------------
>
> This error is being provoked at the top of the .rtp file when a line with
> something like "[header]" is not parsing suitably. A while ago I suggested
> using diff on the .rtp file. Do that.
>
> Mark
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-- 
Yanmei Song
Department of Chemical Engineering
ASU
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