[gmx-users] more x2top troubles

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 17 20:32:55 CEST 2006

Steven Kirk wrote:
> Hello,
> 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:
> http://datavet.hv.se/personal/SK/sio.pdb
> http://datavet.hv.se/personal/SK/sio.top.gz
> http://datavet.hv.se/personal/SK/ffoplsaa.n2t
> 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
Maybe we can move this question to bugzilla, I have already opened one:

please upload the files there, and let's try to work towards a more 
general x2top.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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