Re: Re: Re: how to constrain a dihedral angle?

From: Leonardo G. Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Tue Mar 28 2006 - 16:44:24 CST

On Tue, Mar 28, 2006 at 10:20:02PM +0800, xiaojing gong wrote:
> Hi Leo
> It is so sweet of you to give me that detail, thank you very very very
> very much! I follow your advice, change the parameter file
> par_all27_prot_lipid.inp , replace the name of ARG197 with ARGC197.
> and it can run! BUT I still have three questions:
>
> 1) What the difference betwween par_all27_prot_lipid.inp and
> par_all27_prot_na.prm? that is to say, in which situatuation, I can
> use the par_all27_prot_na.prm.

As the name suggests, the first contains parameters for proteins and
lipids, and the second for proteins and nucleic acids. The protein
parameters are the same, and the same as in the charmm22 version, AFAIK.
Well, there's the CMAP correction for proteins now, but NAMD does not
support the CMAP parameters yet.

> 2) How to use 'mutate' command of psfgen, :--( I change the name of
> the specific residue ARG by hand.

If you change the residue name manually in the pdb, you don't need to
use mutate. For info on the 'mutate' command, please look at the psfgen
user guide.

> 3) When I check the improper dihedral in the top file, I found that
> are more than one need to be changed in parameter file,
>
> CZ CD *NE HE
> CG CA *CB HB1
> CD CB *CG HG1
> CB CG CD NE
> NE CG *CD HD1
>
> but in parameter file, there is only the NC2 X X C for us to change,
> I am confused. I would appreciate it if you could give me some
> suggestions :--)

I didn't really understand what you mean here. Can you try to rephrase
it?

Leo

-- 
Leonardo Giantini Trabuco
Ph.D. student
Center for Biophysics and Computational Biology
University of Illinois at Urbana-Champaign
So it doesn't mess up the flow of reading.
> How come?
> > I prefer to reply inline.
> > > What do you do instead?
> > > > No.
> > > > > Do you like top-posting?

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