[gmx-users] Re: mdrun_make_hole

[Graham Smith]

Itamar Kass wrote:

> My first question deals with the pdb file; the DMPC molecules are
> written as DMP, will GROMACS recognize them when I write #include
> "dmpc.itp" or should I write in the file DMPC?  

I think so, if you work with pdbs I think it only uses the first 3
letters of residue names. (but .gro files support the longer
names...). The file that Bert de Groot posted a few weeks ago will
have what you want won't it? 

> The second question is regarding the script, do I have to cast a
> spell upon the computer before running the script or did I do
> something wrong?

The script can take some options (near the top there's a line that
says # usage make_hole.pl -f 128popw_eq.pdb ... , that gives an
example; I don't know why I didn't just give the script a -h option 
to print that). 

Anyway sounds like you need to say 
make_hole.pl -lipid DMP -f ... and
possibly add also -lipat [something] if the phosphorous isn't called 
P8. 

> My last question is are their any international workshop regarding
> GROMACS in which such methods can be taught?

Not that I know of -- it has to come through years of painful
experience and gigabytes of trajectories containing gibberish. Perhaps
the if there was sufficient demand combined with offers of money the
authors would consider it.

-Graham