[gmx-users] Re: gmx-users Digest, Vol 11, Issue 62

[Jon]

Thanks David, it worked this time. However, I still cannot generate an 
rtp file. I've tried running x2top both with and without a -o X.top 
parameter, when trying to get a -r Y.rtp. ie: 1) x2top -f A.gro -o X.top 
-r Y.rtp 2) x2top -f A.gro -r Y.rtp Where should it save this .rtp file? 
Thanks Jon 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 
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
-------------- next part -------------- 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 ------------------------------