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

Vitaly V. Chaban vvchaban at gmail.com
Sun Jan 17 17:33:04 CET 2010

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?

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.

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