Re: implementing RBCG

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 22 2011 - 21:17:32 CDT

Hi Michael,
There should no longer be any need for a special version of autopsf; the
links you posted are to an old stopgap version that fixed a bug (which
has now been corrected in the main versions).

Could you elaborate on how you tried to build the RBCG models? In order
to help, we need a concrete series of steps from 1ubq.pdb to your error,
because when I try doing this it works fine.

Regarding MARTINI, I know a couple of grad students in Klaus's group
were working on it, but I'm afraid I don't know the current status...
perhaps a current group member could comment.

Best,
Peter

On 03/22/2011 04:11 PM, Michael Zimmermann wrote:
> NAMD Users,
>
> I want to do RBCG simulations on some large systems, but have been
> unable to build RBCG models for small proteins (like 1UBQ) due to
> "/Error: failed on end of //segment; molecule destroyed./" errors.
> These are errors for applying the NTER and CTER patches. If I try to
> set these to NONE then autopsf also fails. Following the advice of:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/11194.html
> and
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14725.html
>
> I have tried to source a different version of autopsf, but I don't see
> how to do so. I have tried to at the tk console, but get: "/conflicting
> versions provided for package "autopsf": 1.3, then 1.2/"
>
> If anyone has further advice on making RBCG models, or a working RBCG
> model that I could learn from, I would appreciate it.
>
> Also, is there any news about using MARTINI in NAMD
> (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8802.html)?
>
> I am using VMD v.1.9 Windows OpenGL, CUDA on 64-bit WinXP.
>
> --
> Michael Zimmermann
> Ph.D. student in Bioinformatics and Computational Biology
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University

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