ADL: I get very high reference RMSD value

曾志平 zengzhiping at xmu.edu.cn
Sun May 11 20:39:08 PDT 2008


you must take care of your initiative coordnative of your ligand,because the 
RMSD is compared with it!
so you had better put your initiative ligand near to the binding site and 
the value of RMSD may lower down. try again1
----- Original Message ----- 
From: "anantha ramanan" <ananthu.bioinfo at gmail.com>
To: <autodock at scripps.edu>
Sent: Sunday, May 11, 2008 6:35 PM
Subject: ADL: I get very high reference RMSD value


> Dear All
>
>               I get very high ref rms value in my docking studies but the
> ligand binds almost near to the crystal binding site. Then i tried to
> specify  the crystal ligand using "refrms" command in DPF but still i am
> getting the same high RMSD value.
> Could anybody let me know the procedure to get low RMSD value.
> Thanks in advance
>
> -- 
> Best Regards
> Anantha ramanan.R
> Junior Scientist,
>
> Institute Of Computational Biology,
> #1101,First Floor , OTC Road,
> Near Corporation Circle,
> Bangalore - 560002
> Visit us at : www.iocbindia.org
> Mail us at : contactus at iocbindia.org
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