[gmx-users] Ligand bond
and.carotti at farmchim.uniba.it
Thu Oct 20 12:54:32 CEST 2005
yes I've used the tutorial way,but with the other steps i've already told.
----- Original Message -----
From: "abelius" <abelius at gmail.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, October 20, 2005 12:06 PM
Subject: Re: [gmx-users] Ligand bond
> I've tried this tutorial before, but they don't make use of a covalently
> bond ligand.
> I was wondering if it were possible to add the ligand to the forcefield
> directly, but I'm not sure how to do that.
> So, did you use your topology as an include without merging it to the
> topology create by pdb2gmx?
> Andrea Carotti wrote:
>> Hi Abelius and Tserjk,
>> I will explain my modus-operandi:
>> in similar situation I've linked (using the specbond.dat file) the
>> proper atoms, then I've completed manually the topology file created
>> using the gromos book,
>> infact some parameters (like angles,bond and dihedrals) are missing.
>> If you want a very good tutorial about drug-enzime complex is here
>> For the perl module, sincerely I don't know nothing about that.
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