[gmx-users] Re: using x2top to convert a gro file to a top file

[Justin A. Lemkul]

Vitaly Chaban wrote:
> Amanda,
> 
> X2TOP is a somewhat enigmatic tool. You are never sure when it why it
> works or refuses to generate a topology...
> 
> Try to start with PDB file instead of GRO. Try to use -"pbc" keyword.
> Try to add new lines to N2T database corresponding to all atoms of
> your molecule.
> 

The -pbc option is broken in the 4.0.x series and will cause the program to hang 
in every case I've seen it invoked.  You must use -nopbc to get the program to 
complete.

-Justin

> Good luck,
> Vitaly
> 
> 
> 
> 
>> I have tried to convert this file to a top file but this is the error message I
>> get:
>>
>> Opening library file /usr/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/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 /usr/share/gromacs/top/vdwradii.dat
>> Entries in vdwradii.dat: 28
>> Opening library file /usr/share/gromacs/top/dgsolv.dat
>> Entries in dgsolv.dat: 7
>> Opening library file /usr/share/gromacs/top/electroneg.dat
>> Entries in electroneg.dat: 71
>> Opening library file /usr/share/gromacs/top/elements.dat
>> Entries in elements.dat: 218
>> Looking whether force field files exist
>> Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
>> Opening library file /usr/share/gromacs/top/ffoplsaa.n2t
>> Opening library file /usr/share/gromacs/top/ffoplsaa.n2t
>> There are 23 name to type translations
>> Generating bonds from distances...
>> atom 48
>> Can not find forcefield for atom C-4 with 2 bonds
>>
>> -------------------------------------------------------
>> Program x2top, VERSION 4.0.7
>> Source code file: ../../../../src/kernel/x2top.c, line: 207
>>
>> Fatal error:
>> Could only find a forcefield type for 47 out of 48 atoms
>> -------------------------------------------------------
>>
>> "Throwing the Baby Away With the SPC" (S. Hayward)
>>
>> I have tried to adjust the coordinates within the gro file but it still shows
>> the same message. Someone please give me some proper instruction in the
>> conversion of a .gro file to a .top file. Thank you!
>>
>> Sincerely,
>>
>> Amanda M. Watkins
>>
>> SBC 2012

-- 
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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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