[gmx-users] Re: Problems with x2top

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 10 13:35:39 CEST 2006

Steven Kirk wrote:
> Hello David,
> I am having some major problems with x2top. I have a PDB file containing 
> atomic coordinate data for a silica nanoparticle, which I want to 
> convert to a valid topology using the OPLS-AA force field. Using the 
> latest version of GROMACS (3.3.1), I tried the x2top command, having 
> previously made sure that all of the atom names in my PDB file were in 
> uppercase. Using the seemingly reasonable ffoplsaa.n2t file:
> O       OH      2       SI      H                       ; SILANOL OXYGEN 
> (OH)
> O       OH      1       SI                              ; Floating O-
> O       OS      2       SI      SI                      ; SILANOL BRIDGE 
> Si-o-Si
> O       OS      3       SI      SI      *              ; don't know what 
> this is
> H       HO      1       O                               ; HYDROXYL HYDROGEN
> SI      SI      4       O       O       O       O       ; SILICON
> SI      SI      5       O       O       O       O       *       ; don't 
> know what this is
> (this was built up from scratch just by trial and error)
> a few problems arise, namely:
> 1. Most of the O atoms in the structure are SI-O-SI bridging atoms, 
> which should be identified as type OS, but instead get identified as 
> type OH
> 2. Looking at the [atoms] section in the generated topology, the masses 
> of all atoms except SI seem to be set to 12 (even the hydrogens!
> I would be very grateful for some advice on how to get a correct 
> topology (with masses, charges and types set correctly). The structure 
> is probably a little big for PRODRG.
> I have tried many things to fix this problem, checking the generated 
> .tpr files to see if the contain the correct masses etc., but they don't.
> Many thanks in advance for your help,
> Steve Kirk
Hi Steve,

we have been thinking about how to improve things in x2top. First, right 
now the the n2t is parsed in a first match mode, so if you swap the 
second and third line things should improve. Second, we should obviously 
change the algorithm to a best-match. Third, the n2t file should have 
some information about expected bond lengths, IIRC this is hard-coded... 
An old reoccurring problem this, you write some software for your own 
use and all of a sudden people start using it as well and all kinds of 
flaws turn up. P.S. let's continue on the mailing list, if only for the 
sake of archiving.

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

More information about the gromacs.org_gmx-users mailing list