[gmx-users] pdb2gmx

[w.j.schravendijk at students.pharm.uu.nl]

> 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).

I ment that I would like to see pdb2gmx do the puzzling for me :)
Sinve it doesn't, the solution would be, as Berk said, to translate my
.top into a ff***.rtp entry. That would still require some puzzling, but
only once.

Greetings, Pim

On Mon, 11 Mar 2002, Anton Feenstra wrote:

> 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?
>
>
> --
> Groetjes,
>
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
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