[MMTK] Amber parameters for ligands

Lars Skjærven larsss at gmail.com
Wed Nov 19 16:46:03 UTC 2008


so the following would be the way to go?

for each atom in ligand:
     atom.amber_charge = 'charge_from_amber_prep_file'
     atom.amber_atom_type = 'atom type from amber prep file'

Would MMTK then know the topology, and thus we would be "set to go"
for minimization?

A more general way would be cooler though. What would I need in order
to build a script that automatically builds MMTK database files from
amber topology files ? Will it not be rather straight forward? I guess
there is a reason for why you did not do it fully automatically, so
there is something I don't see yet.

Lars

On Wed, Nov 19, 2008 at 4:53 PM, Konrad Hinsen <hinsen at cnrs-orleans.fr> wrote:
> Hi Lars,
>
>> I sent an e-mail to the MMTK mailing list 1.5 hours ago, but it has
>> not been distributed yet. I realise now that there has not been mails
>> from the mailing list since the 6th of November. Sounds like something
>> the list is down at the moment...?
>
> Your message is in the archives:
>
>        http://starship.python.net/pipermail/mmtk/2008/001468.html
>
> It is indeed the first one since November 6. 1.5 hours is not unusual for a
> mailing list delay, so perhaps everything is working fine.
>
>> Anyway, I'm eager to proceed.. so I send you the mail directly. maybe
>> you have a quick comment on my topic.
>
> I do, but you won't like it ;-)
>
>> MMTK can nicely read the frcmod (parameter) file. Is there any methods
>> for reading the prep (topology) file as well? That is, to
>> automatically build the molecule file in MMTK/Database/Molecules from
>> the Amber prep file?
>
> There is nothing like that in MMTK. The original MMTK database files were
> generated semi-automatically from the Amber topology files, but the script
> from back then was lost in a disk crash, and I think the Amber format has
> changed since then.
>
>> Am I correct that building the molecule file is all that needs to be
>> done in order to simulate with a ligand as long as the amber parameter
>> file (frcmod) is present?
>
> Yes. You don't even strictly need the database file, you could as well
> assign the Amber atom type and partial charge to your atom objects directly.
>
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hinsen at cnrs-orleans.fr
> Web: http://dirac.cnrs-orleans.fr/~hinsen/
> ---------------------------------------------------------------------
>
>
>
>



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