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

[Vitaly Chaban]

Yes, yes... I mixed them up again... One should try that option which
is not default.


> 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
>
> --
> ========================================
>
> 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
>
> ========================================
>