[gmx-users] problem in recognising the atom type

[Mark Abraham]

gurpreet singh wrote:
> Thanks Mark
> 
> You said OS is not defined in 43a1 force field, so is their any way out 
> for that or i have to use a different force field.

Before your email, I had no idea whether OS was defined in 43a1. You can 
learn about how to find this out for yourself by reading chapter five of 
the manual, and then referring to the .atp file.

If I had a hundred dollars for every time I'd said "read chapter five" 
this year I'd have not needed to bother working!

> Actually i tried using the OPLS force field but in that case i was 
> getting the similar error but this time at the CH3 atom.
> ie 'CH3 atom not found'

If you'd read the documentation for PRODRG, you'd know what force field 
it tries to generate parameters for.

If you'd done some background reading on MD, you'd know not to mix and 
match force fields. It's been five days since I last posted these links, 
so I guess it's time to post them again.... 
http://wiki.gromacs.org/index.php/Parameterization 
http://wiki.gromacs.org/index.php/Force_Fields

> Which is the better force filed for these types of simulation involving 
> these organic compunds ?

That depends what you're trying to measure, the software packages you're 
prepared to use, the kind of compounds you're doing it for, how much 
accuracy you need, and how much you're prepared to spend. There's no 
substitute for reading textbooks and/or original literature here.

Mark