[gmx-users] Re: termini database

[Anton Feenstra]

Y U Sasidhar wrote:
> 
> However, I don't have CH3CO, NHCH3 'residues' in pdb file, i.e, I don't
> have their coordinates in pdb file. That's why I want to add these to
> .tdb files for gromos force field so that pdb2gmx will add these.

That will very likely not work. The implementation of pdb2gmx to add
atoms and generate 'new' coordinates is very limited. But you should
try, it might work. The .tdb files are similar in setup to the .hdb
(hydrogen database). Both are described in some detail in the 
.ps/.pdf/paper manual.

Alternatively, use any available protein modeling software to add an
additional residue to your molecule, and remove any of the atoms that
you don't need. It doesn't matter if the coordinates are not precisely
right (i.e. wrong bond lengths or angles, as long as atoms are not on
top of each other), since a simple energy minimisation step will fix
that.

-- 
Groetjes,

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