Re: formyl and ethanolamide parameters and topology

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Thu Jun 23 2011 - 12:08:58 CDT

Hi,

I normally use the following protocol:

1) Search for your molecule at Pubchem and copy the SMILES format of it.

2) Go to the Zinc database (http://zinc.docking.org/) and use the SMILES format to search and download the *.mol2 version of the molecule.

   Alternatively uou may use Quimera software to generate Hydrogens and save as *.mol2 from a simple *.pdb file.

3) Then, go to the Swiss Param (http://swissparam.ch/) and use the *.mol2 file to generate parameters and topology of interest.

OBS: Note that inside of the topology file the name of the residue will be LIG, independently of the molecule, and you must change it before use.
 
I hope it can help.

Dr. Flavio Augusto Vicente Seixas
Professor Adjunto do Departamento de Bioquímica - DBQ
Universidade Estadual de Maringá - UEM
Av. Ângelo Moreira da Fonseca, 1800 - Zona 7
87506-370 - UMUARAMA - PR - BRAZIL

--- On Thu, 6/23/11, Jorgen Simonsen <jorgen589_at_gmail.com> wrote:

> From: Jorgen Simonsen <jorgen589_at_gmail.com>
> Subject: namd-l: formyl and ethanolamide parameters and topology
> To: namd-l_at_ks.uiuc.edu
> Date: Thursday, June 23, 2011, 3:52 PM
> Hi all,
>
> I have looking for the formyl and ethanolamide parameters
> and topology
> which have been used in one of the tutorial in the
> simulation of
> gramacidin but I have not been able to locate these?
>
> Any ideas?
>
> Thanks,
>
>

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