[gmx-users] pdb2gmx

[Anton Feenstra]

w.j.schravendijk at students.pharm.uu.nl wrote:
> 
> Dear gromacs-people,
> 
> Shouldn't it be a useful option to enable the selection of additional .top
> or .itp files as an input for pdb2gmx, so pdb2gmx can automatically sort
> and process this input when non-protein molecules are present?

I'm not sure if I understand exactly what you mean. But one thing
you *can* already do, is copy the relevant ff*.* files to your local
directtory, and also copy the FF.dat file. That last file contains
the list of forcefields that pdb2gmx will let you choose from. If you
rename the local forcefield files (ff*.*) and add a line to your local
FF.dat, you can probably get more or less what you suggest?

If you have a system whit protein and 'other' molecules, you can always
process them in pdb2gmx separately, and put the .top and .gro files
together manually (takes some puzzling, though).

-- 
Groetjes,

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