From: David van der Spoel <[EMAIL PROTECTED]> Subject: [gmx-users]
Re: Problems with x2top To: Steven Kirk <[EMAIL PROTECTED]>,
Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID:
<[EMAIL PROTECTED]> 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 ?
Regards,
Steve Kirk
--
Dr. Steven R. Kirk <[EMAIL PROTECTED], [EMAIL PROTECTED]>
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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