[gmx-users] g_mindist command doubt???????

[Tsjerk Wassenaar]

darn, that should have read:

[ NTERM ]
1
[ CTERM ]
288

:p

On 9/14/05, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> Hi Rahul,
> 
> Make an index file with two groups: 
> 
> [ CTERM ]
> 1
> [ NTERM ]
> 288
> 
> and use that with g_mindist.
> 
> Cheers,
> 
> Tsjerk
> 
> On 9/14/05, Rahul Karyappa <r.karyappa at ncl.res.in> wrote:
> 
> > Dear all, 
> > I want to know the end-to-end distance of my chain which is surrounded 
> > by ions and water molecules. I used g_mindist command to get the values. But 
> > I am confused while selecting the groups. The following window occurs:
> > 
> > How many other groups do you want (>= 1) ?
> > 1
> > Reading file topol.tpr, VERSION 3.2.1 (single precision)
> > Reading file topol.tpr, VERSION 3.2.1 (single precision)
> > Opening library file /usr/local/gromacs/share/top/aminoacids.dat
> > Group 0 ( System) has 9369 elements
> > Group 1 ( Protein) has 288 elements
> > Group 2 ( Protein-H) has 288 elements
> > Group 3 ( C-alpha) has 0 elements
> > Group 4 ( Backbone) has 0 elements
> > Group 5 ( MainChain) has 0 elements
> > Group 6 (MainChain+Cb) has 0 elements
> > Group 7 ( MainChain+H) has 0 elements
> > Group 8 ( SideChain) has 288 elements
> > Group 9 ( SideChain-H) has 288 elements
> > Group 10 ( Prot-Masses) has 288 elements
> > Group 11 ( Non-Protein) has 9081 elements
> > Group 12 ( SOL) has 9081 elements
> > Group 13 ( Other) has 9081 elements
> > 
> > But how to choose the groups?
> > Waiting for your kind reply.
> > 
> > Rahul Karyappa
> > NCL, Pune
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> 
> 
> -- 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336 




-- 
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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