From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Thu Jun 23 2011 - 21:58:27 CDT
Hi Han,
Normally I do not use the psf file generated by the
server.
I use the Automatic psf builder within VMD to generate a
new.
Just include the topology file of the small molecule into
the appropriate tab with the topology that already exists.
Then, generate new psf files to your molecule or complex.
The topology file generated by SwissParam has a text
extention, maybe a *.rtf file (I do not remember now).
I think the problem you faced is because you are not using
the appopriate topology file for your ligand.
Regards,
Flavio
> --- On Thu, 6/23/11, Shen, Han <han.shen_at_bme.gatech.edu>
> wrote:
>
> > From: Shen, Han <han.shen_at_bme.gatech.edu>
> > Subject: Re: namd-l: formyl and ethanolamide
> parameters and topology
> > To: "flavio seixas" <oivalf_nix_at_yahoo.com>
> > Date: Thursday, June 23, 2011, 11:40 PM
> > Thanks Flavio! The protocol really
> > helps a lot!
> >
> > I tried it to get topology and parameters files for
> my
> > molecular, and got .psf .pdb .par .itp(I don't know
> what is
> > itp file). The psf and pdb files can be loaded in
> VMD,
> > however, when I tried to solvate the molecular into a
> water
> > box, an error came out said that:
> >
> > reading structure from psf file ***.psf
> > error reading atoms
> >
> > Does anyone know what is the problem or has any
> > suggestions?
> > Thanks,
> >
> > Han
> >
> > ----- Original Message -----
> > From: "flavio seixas" <oivalf_nix_at_yahoo.com>
> > To: namd-l_at_ks.uiuc.edu,
> > "Jorgen Simonsen" <jorgen589_at_gmail.com>
> > Sent: Thursday, June 23, 2011 1:08:58 PM
> > Subject: Re: namd-l: formyl and ethanolamide
> parameters and
> > topology
> >
> > 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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