[gmx-users] analysis tools...

[David]

On Sat, 2003-06-14 at 06:44, Swetha Vijayakrishan wrote:
> hi gmx users,
> 
> i just wanted to know if gromacs has any tool that can calculate the rmsd
> as a function of residue number?
actually you can do it with g_rms, but not very efficient.  just fit on
all Calphas and compute rmsd for all residues separately. you will get N
files for N residues. You probably want something like a pdb file color
coded (b-factor) by rmsd?


> Also can a plot of the psi and phi angles  v's time  be done for any
> specific residue?
Yes that's in g_chi


> Would really appreciate if anyone is aware of  how these
> can be implemented in gromacs.
> 
> Thanks
> 
> swetha
> 
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> *******************************************************************************
> 
> 
> Swetha Vijayakrishnan
> 
> Project Assistant
> C/O Dr.Shekhar.C.Mande
> Centre for DNA Fingerprinting and Diagnostics(CDFD),
> ECIL Road,Nacharam,
> Hyderabad - 500076
> 
> Phone:: Direct: 91-040-7171442
>         Indirect: 91-040-7151344/46/47/56 (lab extn 1400)
> 
> Fax  :: 91-040-(7155479-7155610>
> 
> Email:: swetha at cdfd.org.in
>         swethasenorita at yahoo.com
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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