thank you for the suggestion. It has worked :)
On Mon, Dec 19, 2011 at 5:12 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Use this
>
> rms mass reference out 1fm9_far_H-12_backbone_time time 2.0 :278-288.CA
> ,C,N
>
>
> > Dear Amber community member,
> > I'm having trouble calculating RMSD vs time.
> > I have done successfully RMSD vs frames.
> >
> > The 3ns MD input file and input for ptraj are given below.
> > Please suggest what modifications will give me RMDS values vs. time.
> >
> > Ptraj input file
> > ---------------
> > trajin /home/vaibhav/vaibhav_data/
> > amber/1fm9_far/1fm9_MD_runs/1fm9_far_3nMD_1.mdcrd 15 1500 1
> >
> > reference
> >
> /home/vaibhav/vaibhav_data/amber/1fm9_far/1fm9_MD_runs/1fm9_far_equil.restrt
> >
> > rms mass reference out 1fm9_farallbackbone_time '.CA,C,N' time 0.5
> >
> > rms mass reference out 1fm9_far_H-12_time ':278-288' time 0.5
> >
> > rms mass reference out 1fm9_far_H-12_backbone_time ':278-288 & @CA,C,N'
> > time 0.5
> > -------
> > I tried using time 1.0 and time 2.0.
> > Without time command it gives RMSD vs. frame which is OK for my purpose
> >
> > 3nd MD input file
> > -----
> > 3ns MD 1fm9_far complex
> > &cntrl
> > imin=0,irest=1,ntx=5,
> > nstlim=1500000,dt=0.002,
> > ntc=2,ntf=2,
> > cut=8.0, ntb=2, ntp=1, taup=2.0,
> > ntpr=1000, ntwx=1000,
> > ntt=3, gamma_ln=2.0,
> > temp0=300.0,
> > /
> > ------
> >
> > Thank you all.
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
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>
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>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Mon Dec 19 2011 - 05:30:08 PST
