[gmx-users] x2top hangs

[Justin A. Lemkul]

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
> smilner at engr.psu.edu
> 
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-- 
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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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