[gmx-users] itp file

[Anton Feenstra]

jozef hritz wrote:
> 
>         Dear Anton,
> 
> I found Your script and used it. It shows that in simulation are no L-J
> parameters as well as no atom masses. They are not included in
> newmolecule.itp file but I thought they will be included from ffgmx.itp
> file on the base of atom types. Why then are atom types used when all
> parameters are required?

LJ parameters and masses are not parsed by the script. To check those,
I suggest you follow David's suggestion (see his reply...)
They should indeed be included from the ffgmx.itp files, for which 
indeed the atom types are used. I don't know what you mean when you
say 'all parameters are required'. They are not.

> The next things is that in my newmolecule.itp file type of function for
> bonding and bending I have 1 and for dihedrals 1 or 2 but output of Your
> script shows type 3 for all of them.

That is probably a stupid bug. I just had a look, but couldn't find
the problem right away...
The script isn't intended as a replacement for grompp, obviously.
But sometimes, when de-bugging a topology file you wrote yourself
it can be handy to see exactly whcih atoms are actually used in
each of the interactions, and to see all parameters explicitly.
In fact, we could use a tool that does this and much more to
facilitate topology debugging work. For example, it would be nice
to also get an energy value for each interaction based on the 
starting coordinates. Errant interactions would show up with high
energies immediately. I believe I've heard David mention he has
something in that direction?

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
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