did you have a look at your trajectories using an visualizer???
Perhaps VMD or chimera can be helpful.
Best Regards
[photo]
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
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________________________________
From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
Sent: 14 May 2017 22:43:54
To: AMBER Mailing List
Subject: [AMBER] dimer rmsd issue.
Dear All,I have plotted dimer rmsd using following command;parm *.prmtoptrajin md_simulation?.mdcrdtrajin md_simulation??.mdcrdautoimagestrip :Na+,WAT outprefix nowater
rms first out rmsd.dat :1-534.C,CA,Ntrajout AD-chain_complex-reimaged-20ns.nc netcdf
I also tried another command which was suggested in amber archive (
http://archive.ambermd.org/201109/0749.html) to improve rmsd;
parm *.prmtoptrajin md_simulation?.mdcrdtrajin md_simulation??.mdcrdcenter :1-267 mass origin
image origin center familiarcenter :1-534 mass originimage origin center familiarstrip :Na+,WAT outprefix nowaterrms first out rmd.dat :1-534.C,CA,Ntrajout AD-chain_complex-reimaged-20ns.nc netcdf
got same result. RMSD plot image attached here. Does anybody know how I might fix the RMSD values Any suggestion would be really appreciated.
Thanks
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Received on Sun May 14 2017 - 11:00:02 PDT
