[gmx-users] Re: Problems with x2top

[David van der Spoel]

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.

Regards,
-- 
David.
________________________________________________________________________
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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