q=D8=B8=B4=A3=BA=20=20Re:=20Re=A3=BA=20Re:=20?= qhow=20to=20constrain=20a=20dihedral=20angle=3F?=

From: xiaojing gong (gongxiaojing1981_at_yahoo.com.cn)
Date: Wed Mar 29 2006 - 06:31:46 CST

     I mean that there is eight improper dihedrals needed to change name of atom type,
  IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163
IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124
  IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121
IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143
  IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143
IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150
  IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065
  IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292
  BUT in the parmeter file, there is only NC2C X X C , so I am a little confused.
  "Leonardo G. Trabuco" <ltrabuco_at_ks.uiuc.edu> д
  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,
> 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


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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