[gmx-users] x2top - wrong mass in .top file

[David]

On Tue, 2005-03-22 at 13:37 -0500, Jon wrote:
> Hello Users
> 
> I am trying to make a topology file of a quartz surface, from a 
> coordinate file (.gro) that I generated myself. I started with a single 
> unit cell of quartz (SiO2)_3, and am using the GMX force field. After 
> modifying the .n2t file so that x2top would run, it generated a .top 
> file. The mass of Silicon is fine (28.080), but the mass of the oxygen 
> is set at 12, not the 15.99 that is set in ffgmx.atp.
> 
> I am using standard atomtypes (OS for oxygen, SI for silicon). I had to 
> play around with the n2t file, such that some of the bonding is not 
> realistic, and there are no hydrogens, but this is just a first attempt, 
> so its okay for now.
I have previously used attached n2t file for quartz. Maybe it helps.
-- 
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://xray.bmc.uu.se/~spoel
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O	O	1	C				; CARBONYL OXYGEN (C=O)
O	OM	1	C				; CARBOXYL OXYGEN (CO-)
O	OS	2	SI	SI
O	OA	2	H	SI			; HYDROXYL OXYGEN (OH)
O	OW	2	H	H			; WATER OXYGEN
N	N	3	H	C	C		; PEPTIDE NITROGEN (N OR NH)
N	NT	3	H	H	C		; TERMINAL NITROGEN (NH2)
N	NL	4	C	H	H	H	; TERMINAL NITROGEN (NH3)
N	NR5	2	C	C			; AROMATIC N (5-RING,2 BONDS)
N	NR5*	3	C	C	H		; AROMATIC N (5-RING,3 BONDS)
N	NP	3	C	C	FE		; PORPHYRIN NITROGEN
C	C   	3	C	O	*		; BARE CARBON (PEPTIDE,C=O,C-N)
; Note that order is importante here because of wildcards.
C	C3	4	H	H	H	*	; ALIPHATIC CH3 GROUP
C	C2	4	H	H	C	*	; ALIPHATIC CH2 GROUP
C	C1   	4	H	C	*	*	; ALIPHATIC CH GROUP
C	CB  	3	C	C	C		; BARE CARBON (5-,6-RING)
H	H   	1	N	 			; HYDROGEN BONDED TO NITROGEN
H	HO  	1	O	 			; HYDROXYL HYDROGEN
H	HW  	1	OW	 			; WATER HYDROGEN
H	HS  	1	S	 			; HYDROGEN BONDED TO SULFUR 
H	HC  	1	C	 			; HYDROGEN BONDED TO CARBON
SI	SI	4	O	O	O	O
SI	SI	3	O	O	O
SI	SI	2	O	O