[gmx-users] x2top

[Justin A. Lemkul]

Bernhard Knapp wrote:
> Dear Users
> 
> I tried to use the x2top function of gromacs 4 on a sugar-molecule. But 
> the gromacs says that it requests the ffgmx.n2t library which can not be 
> found in the default directory. I searched in the whole system but could 
> not find it. Therefore I also searched on an other system with gromacs 
> 3.3 and copied the file form there to the system with gromacs 4. 
> Unfortunately it comes up with the next request as below:
> -------------------------------------------------------
> Program x2top, VERSION 4.0
> Source code file: futil.c, line: 527
> 
> Fatal error:
> Library file ffG43a1.n2t not found in current dir nor in default 
> directories.
> (You can set the directories to search with the GMXLIB path variable)
> -------------------------------------------------------
> But I could not find this file neigther on the gromacs 4 nor on the 
> gromacs 3.3 system ...
> 
> Where can I get all those n2t files from? Or am I doing something wrong? 

As with all topologies and many data files, they are in the /share/top directory 
of your installation.  There are two available: ffG53a5 and ffoplsaa.

> My command is simply:
> x2top -f sed.pdb -o sed.top -ff select
> with forcefield 0:GROMOS96 43a1 force field
> if i use 5: OPLS-AA/L it writes
> "Generating bonds from distances...
> atom 0" to the command line and gets stuck
> 

I believe x2top version 4.0 is under heavy development, and may not be fully 
functional in its current form.  It looks like your coordinate file is from 
PRODRG; why not use PRODRG to generate a rough topology, and refine it according 
to the ffG43a1 parameters?

-Justin

> where sed.pdb contains only
> HETATM    1  CAA DRG     1      -8.720   2.440  -1.910  1.00 
> 20.00             C
> HETATM    2  OAB DRG     1      -8.220   1.420  -2.790  1.00 
> 20.00             O
> HETATM    3  CAC DRG     1      -9.020   0.470  -3.380  1.00 
> 20.00             C
> HETATM    4  OAD DRG     1      -8.430  -0.270  -4.170  1.00 
> 20.00             O
> HETATM    5  CAF DRG     1     -10.540   0.220  -3.190  1.00 
> 20.00             C
> HETATM    6  OAE DRG     1     -11.330   1.410  -3.060  1.00 
> 20.00             O
> HETATM    7  CAG DRG     1     -10.840  -0.720  -2.000  1.00 
> 20.00             C
> HETATM    8  OAH DRG     1     -10.270  -0.190  -0.800  1.00 
> 20.00             O
> HETATM    9  CAI DRG     1     -10.330  -2.150  -2.280  1.00 
> 20.00             C
> HETATM   10  OAJ DRG     1     -10.940  -2.650  -3.470  1.00 
> 20.00             O
> HETATM   11  CAK DRG     1     -10.620  -3.170  -1.170  1.00 
> 20.00             C
> HETATM   12  OAL DRG     1     -11.900  -2.940  -0.570  1.00 
> 20.00             O
> HETATM   13  CAM DRG     1      -9.550  -3.150  -0.060  1.00 
> 20.00             C
> HETATM   14  OAN DRG     1      -9.840  -4.150   0.920  1.00 
> 20.00             O
> 
> 
> Is this a problem of gromacs or am I really missing libraries or is the 
> input somehow bad?
> 
> 
> sincerely
> Bernhard
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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