[gmx-users] D-L conversion!

[David van der Spoel]

On Wed, 2003-08-27 at 02:22, Swetha Vijayakrishan wrote:
> hi all,
> 
> I had run a 2 nanosecond MD using Charmm.
> Now i find a few of the residues having their chirality changed from L to
> D especially the Prolines.
> Is this very common in MD? Or have i made some mistake.
> Does anybody know how i can rectify this problem without rerunning the MD
> again??
No, if your protein is in a wrong conformation than you should rerun the
simulation. In this case you want to check whether there is an improper
dihedral on the Ca in the Prolines.

> 
> 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 & Mol. 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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