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 <vvcha...@gmail.com>
Date: Sun, Jan 17, 2010 at 6:27 PM
Subject: x2top(4.0.7)
To: gmx-users@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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
