Scott Milner wrote:
Folks -- I cannot manage to get x2top to work on even the simplest example.
Here is "ethane.pdb", a PDB file for ethane (built using Avogadro, with
the CONECT records stripped out):
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.2.2b1
ATOM 1 C LIG 1 -3.466 -1.641 -0.001 1.00
0.00 C
ATOM 2 C LIG 1 -1.954 -1.689 0.025 1.00
0.00 C
ATOM 3 H LIG 1 -3.817 -0.605 0.026 1.00
0.00 H
ATOM 4 H LIG 1 -3.882 -2.168 0.863 1.00
0.00 H
ATOM 5 H LIG 1 -3.850 -2.112 -0.910 1.00
0.00 H
ATOM 6 H LIG 1 -1.570 -1.218 0.934 1.00
0.00 H
ATOM 7 H LIG 1 -1.538 -1.163 -0.839 1.00
0.00 H
ATOM 8 H LIG 1 -1.603 -2.726 -0.002 1.00
0.00 H
END
I try to run the following command under GROMACS 4.0,
x2top -f ethane.pdb -o ethane.top
with the most recent version of the file ffoplsaa.n2t in its proper
place (/usr/local/gromacs/share/gromacs/top/),
and I get the following output:
...
Opening library file /usr/local/gromacs/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/local/gromacs/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/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Looking whether force field files exist
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t
There are 23 name to type translations
Generating bonds from distances...
atom 0
... and then the program hangs.
Can someone confirm that x2top actually works, and send a simple working
example to me?
The 4.0.x versions of x2top do not work, as far as I know. The code is
undergoing major changes. Version 3.3.3 should be operable, if memory serves.
-Justin
Scott Milner
William H. Joyce Professor
The Pennsylvania State University
Department of Chemical Engineering
120 Fenske Laboratory
University Park, PA 16802
(814) 863-9355
smil...@engr.psu.edu
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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