[gmx-users] Re: problems with x2top

Steven Kirk Steven.Kirk at hv.se
Tue Apr 11 16:41:38 CEST 2006

> From: David van der Spoel <spoel at xray.bmc.uu.se> Subject: [gmx-users]
> Re: Problems with x2top To: Steven Kirk <Steven.Kirk at hv.se>,
> Discussion list for GROMACS users <gmx-users at gromacs.org> Message-ID:
> <443A430B.1060108 at xray.bmc.uu.se> Content-Type: text/plain;
> charset=ISO-8859-1; format=flowed 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.

I suppose one way to partly solve the problem would be to somehow get 
x2top to respect CONECT records in the PDB file to indicate the presence 
of bonds, then hand over the responsibility for generating these CONECT 
records on the basis of interatomic distances to an external program 
(does anyone know if, e.g. OpenBabel can generate these records ?).

The matching of types to names should definitely be made 'best-match', 
yes. I have edited my PDB file so that there are two distinct oxygen 
names (OS and OH), removed numerical digits from the names of my H 
atoms, then constructed a new topology using a .n2t file generated by 
iterating the 'run, fix error message' cycle.

So now the types listed in the topology are fine, but the masses, 
charges and force field parameters are still broken.

Does x2top look up the mass based on the name, the type or the raw 
element symbol ?

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

More information about the gromacs.org_gmx-users mailing list