[gmx-users] more x2top troubles

Steven Kirk Steven.Kirk at hv.se
Sun Apr 16 19:22:16 CEST 2006


First, let me thank all those who have contributed helpful suggestions 
here in the past, especially DvS.

I am having major problems generating a topology using x2top that 
contains valid data in the [bonds], [angles] and [dihedrals] sections.

The files I use can be downloaded here:


The PDB file contains a 711-atom silica cluster centered in a 6nm box, 
with the surface passivated with H atoms except for 9 sites where the H 
atoms have been removed (leaving, notionally, a deprotonated silanol 
group). I intend to hand-edit the [atoms] section of my topology later 
so I can give these O atoms a -1 charge, fill the box with water and add 
9 Na+ ions to the system for charge neutrality, but the charge issue is 
in the future ..

Having copied the FF.dat, ffoplsaa.{itp, rtp, atp}, ffoplsaanb.itp and 
ffoplsaabon.itp files from the installation directory to the current 
working directory, I edited the new types OS, OH and HO into the 
ffoplsaanb.itp file, copying the data for opls_179, opls_154 and 
opls_155 respectively and setting the charge field to 0.0.

Having done this, the command (Linux x86_64, Gromacs release version 3.3.1)

GMXLIB=. x2top -f sio.pdb -o sio.top -name SNP -param -debug

gives the topology file listed above.

The masses have been copied into the topology OK, but x2top generates a 
[bonds] section that looks like this:

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
     1   421     1  1.560000e-01  4.000000e+05  1.560000e-01  4.000000e+05

i.e. it seems to ignore the [bondtype] information provided at the 
bottom of the ffoplsbon.itp file (edited in by DvS) describing what a 
SI-OS bond should be like. This doesn't match with my expectations, 
because there seem to be 4 parameters present (two of which are the 
defaults for the -kb command line option) when I expected two, namely 
'b0' and 'kb' with values taken from the ffoplsaabon.itp file.

The [angles] and [dihedrals] sections are similarly broken (but the 
latter might be because the [dihedraltypes] section right at the end of 
ffoplsaabon.itp seems to have too few parameters listed? Can the 
developers check this?)

I would greatly appreciate any advice from anyone on this list on how to 
fix this. I have read and re-read the manual many times and have 
searched the mailing lists, but can find no solution.

Are there any other 3rd-party tools in existence that can generate a 
valid topology (calculating [bonds], [angles] and [dihedrals] 
information) for non-organic systems with this number of atoms (possibly 
even by translation from other MD software's topology files ?)

To the experts: Is there a way of using a topology file with at least a 
valid [atoms] section to produce e.g. a .tpr run file, then feeding back 
the .tpr file generated as an input to x2top in an attempt to get valid 
[bonds], [angles] and [dihedrals] sections in a 2-pass approach? I have 
attempted this, with no success ..

*VERY* many thanks in advance for any advice you can provide,

Steve Kirk
Dr. Steven R. Kirk           <Steven.Kirk at hv.se, S.R.Kirk at physics.org>
Dept. of Technology, Mathematics & Computer Science  (P)+46 520 223215
University West                                      (F)+46 520 223299
P.O. Box 957 Trollhattan 461 29 SWEDEN       http://taconet.webhop.org

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