[gmx-users] molecule of metane

[Mark Abraham]

foh wrote:
> Thanks you.
> 
> But, that it is necessary to write in 4 column for simple molecules of type methane, ethane
> for OPLS potential ?
> 
> HEADER METHANE
> ATOM      1  CB   ???    1       3.875   0.678  -8.417  1.00  0.00              
> ATOM      2  HB1  ???    1       3.800   1.690  -8.076  1.00  0.00              
> ATOM      3  HB2  ???    1       4.907   0.410  -8.516  1.00  0.00              
> ATOM      4  HB3  ???    1       3.406   0.026  -7.711  1.00  0.00              
> ATOM      5  HB4  ???    1       3.389   0.583  -9.366  1.00  0.00              
> END

I can't understand your question. The point of pdb2gmx is to take a 
structure and a forcefield, look up its topology in the database, and to 
write a consistent .top file (see 
http://wiki.gromacs.org/index.php/.top_file). It only makes sense to 
give it a structure that has a topology that is in its database - and 
not all structures are, obviously.

Read chapter 5 of the manual, read ffoplsaa.rtp and find out whether you 
need to write your .top by hand.

You should also do some tutorial material to get your brain around the 
usual gromacs way of doing things, before you try to work out how to do 
whatever you want to do on the system you're interested in.

Mark