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

[Jon]

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.

Here are excerpts from my gro (input) and top (output) files:

.gro
    1QRTZ    SI    1   0.000   0.246   0.078
    1QRTZ   OS1    2   0.098   0.237   0.208
    1QRTZ   OS2    3   0.026   0.387   0.000
    2QRTZ    SI    4   0.139   0.143   0.334
    2QRTZ   OS1    5   0.008   0.116   0.428
    2QRTZ   OS2    6   0.196   0.000   0.279
    3QRTZ    SI    7   0.348   0.200   0.555
    3QRTZ   OS1    8   0.254   0.217   0.422
    3QRTZ   OS2    9   0.443   0.331   0.571

.top
    [ atoms ]
     1         SI      1   QRTZ     SI      0          0      28.08
     2         OS      1   QRTZ    OS1      1          0         12   
     3         OS      1   QRTZ    OS2      2          0         12    
     4         SI      2   QRTZ     SI      3          0      28.08
     5          O      2   QRTZ    OS1      4          0         12     
     6          O      2   QRTZ    OS2      5          0         12    
     7         SI      3   QRTZ     SI      6          0      28.08    
     8         OS      3   QRTZ    OS1      7          0         12    
     9         OS      3   QRTZ    OS2      8          0         12

Why am I getting the wrong mass (12 instead of 15.99)? As well, I told 
it to make an rtp file, but I cannot find it anywhere. Is this normal? 
My command was "x2top -f X.gro -o Y.top -r Z.rtp -param"

Cheers
Jon


-- 
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Jon Ellis
Thompson Group
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
University of Toronto
LM147 - (416) 978-6568
jon.ellis at utoronto.ca