Re: formyl and ethanolamide parameters and topology

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Fri Jun 24 2011 - 03:52:32 CDT

Hi,

Regarding first part, you can obtain 3D structures from SMILES or 2D
structure by CORINA demo online
(http://www.molecular-networks.com/online_demos/corina_demo). Small
molecules are generated with hydrogens'. Alternatively ACD Chemsketch
(freeware, http://www.acdlabs.com/resources/freeware/chemsketch/) could
convert 2D structures to SMILES. Probably best posibility is to use
VEGAZZ (free, http://www.ddl.unimi.it/) . Program could generate 3D
structure from 2D and have a lot of options to set-up and analyze NAMD
jobs/outputs.

Branko

On 6/23/2011 7:08 PM, flavio seixas wrote:
> 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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