From: Lin (lavizgal_at_yahoo.com.sg)
Date: Tue Feb 07 2006 - 23:53:32 CST
Hi all,
regarding the tutorial, I am trying to use the basic
1JNO.pdb protein downloaded from the tutorial to do a SMD
unfolding by applying forces to the protein. however, i
failed to generate the psf using the autopsf plugin for
the protein as 18 residues/segments were unparameterized,
i tried including the topology files provides in the
Gramicidin A tutorial, but it doesnt seem to help. I
wonder isst becoz the plugin cant read the additional
topology files I have added?
Do correct me if im wrong. Thank you!!
Regards,
Lin
--- "M. Madhu" <madhu7_at_hotmail.com> wrote:
>
> Hi Gumbart,
>
> Thank you very much for your reply. I got both
> top_*.inp and par_*.inp
> files.
>
> Madhu
>
> >From: JC Gumbart <gumbart_at_ks.uiuc.edu>
> >To: "M. Madhu" <madhu7_at_hotmail.com>
> >CC: namd-l_at_ks.uiuc.edu
> >Subject: Re: namd-l: Topology file for Building
> Gramicidin A (tutorial)
> >Date: Tue, 7 Feb 2006 13:20:06 -0600
> >
> >I think they should have been downloaded by VMD in the
> running of the
> >tutorial, but in any case, they are located here:
> >
>
>http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/
>
> >top_all27_prot_lipid.inp
> >
>
>http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/
>
> >par_all27_prot_lipid.inp
> >
> >On Feb 7, 2006, at 11:37 AM, M. Madhu wrote:
> >
> >>Dear NAMD users,
> >>
> >>I am a new NAMD user. I am trying to do the tutorial
> for Gramicidin in
> >>explicit
> >>membrane. In the begining of the tutorail it was
> mentioned that new
> >>entries
> >>were made for formyl and ethanolamide groups in the
> topology file
> >>(toppar/top_all27_prot_lipid.inp). I could not find
> the topology file
> >>with these
> >>two groups. I would appreciate if someone can tell me
> the exact location
> >>of
> >>this file (downloadable) or send me the correct
> topology & parameter
> >>files
> >>for doing this tutorial.
> >>
> >>Thank you very much.
> >>
> >>Madhu
> >>
>
>>_________________________________________________________________
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>
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