[gmx-users] adding a non-residue molecule

[Anton Feenstra]

Valentin Gogonea wrote:
> 
> Hello gromacs users,
> 
> I constructed the topology file (.itp) for a molecule which is not in
> the .rtp file. I run separately pdb2gmx for the protein without cofactor
> and now I want to construct the .tpr file for protein+cofactor. My
> problem is that I have coordinates from a .gro file for protein and from
> a pdb file for cofactor. How can I mix them now? pdb2gmx seems to change
> the coordinates of protein.

It shouldn't, except if you specify -noreth or -ignh (depends on the
version), it will re-calculate hydrogen atom coordinates from its 
internal rules, in stead of using the coordinates from the input files.
It *never* touches coordinates of heavy atoms!

The general way to mix these things, is to split your input files into
the part that can/should be processed by pdb2gmx (e.g. the protein(s)),
and the part that can/should not. Then, into the .top file generated
by pdb2gmx you insert a #include statement for the .itp file of your
'other part' and into the .gro/.pdb file generated by pdb2gmx you
re-insert the 'other part' of your input .pdb/.gro file (use editconf
to convert .pdb to .gro or back if necessary). In effect, you let the
parts pdb2gmx doesn't know about by-pass pdb2gmx.

By the way, isn't this in the FAQ?, it probably should be... 
(couldn't find it, though)


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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