[gmx-users] Fwd: x2top(4.0.7). More.

[Vitaly V. Chaban]

Justin,

Thanks. The problem was that I didn't use "-nopbc" option.

Vitaly


On Sun, Jan 17, 2010 at 7:11 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> And more. What is the algorithm to detect that the proper atom group?
>> Is it based both on the atom names in PDB and interatomic distances?
>>
>> So if we have for example
>> O    opls_236    -0.5   15.9994 1    C 0.123
>>
>> and in the submitted structure r(C-O)=0.126 - what it be recognized?
>>
>
> Details are on the Gromacs wiki:
>
> http://www.gromacs.org/Documentation/Gromacs_Utilities/x2top
> http://www.gromacs.org/Documentation/File_Formats/.n2t_File
>
> If the above doesn't address the original problem (the program hanging),
> please post your actual command line.
>
> -Justin
>
>> Thanks in advance.
>>
>>
>> ---------- Forwarded message ----------
>> From: Vitaly V. Chaban <vvchaban at gmail.com>
>> Date: Sun, Jan 17, 2010 at 6:27 PM
>> Subject: x2top(4.0.7)
>> To: gmx-users at gromacs.org
>>
>>
>> Hi all,
>>
>> What can be the reason that x2top(4.0.7) stops with
>>
>> Looking whether force field files exist
>> Opening library file /root/gromacs.407/share/gromacs/top/ffG53a6.rtp
>> Opening library file /root/gromacs.407/share/gromacs/top/ffG53a6.n2t
>> Opening library file /root/gromacs.407/share/gromacs/top/ffG53a6.n2t
>> There are 0 name to type translations
>> Generating bonds from distances...
>> atom 0
>>
>> Meanwhile the processor load is high at that moment and the utility
>> never finishes itself.
>>
>> --
>> Vitaly V. Chaban, Ph.D.
>> http://www-rmn.univer.kharkov.ua/chaban.html
>
> --
> ========================================
>
> 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
>
> ========================================
>