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

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 17 18:11:47 CET 2010



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

========================================



More information about the gromacs.org_gmx-users mailing list