[gmx-users] Ligand bond

[Andrea Carotti]

Hi,
yes I've used the tutorial way,but with the other steps i've already told.
Bye
Andrea
----- 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


> Hi,
> 
> 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?
> 
> Greetings,
> Abel
> 
> 
> 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
>> http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
>> For the perl module, sincerely I don't know nothing about that.
>> Bye
>> Andrea
>>
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