Dear George,
Try this:
rms reference out equil_0-2ns.rmsd time 1.0 .CA,C,N
Following command had worked for me. It depends on what input you have
given. my input is also shown below for comparison.
rms mass reference out 1fm9_far_H-12_backbone_time time 2.0 :278-288.CA,C,N
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,
/
------
On Wed, Jan 4, 2012 at 11:45 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> I'm measuring the backbone RMSD of a 2ns equilibration trajectory against
> the crystal structure.
>
> Using the VMD RMSD trajectory tool and having as reference the crystal
> structure I obtained the following results:
>
> id mol avg sd
> min max num
> 0 2wc6.pdb 0.000 0.000
> 0.000 0.000 0
> 1 2wch_bal_solv.prmtop 1.222 0.084 0.987
> 1.481 1000
>
> Using the following ptraj input file:
>
> trajin equil_2ns.mdcrd.gz 1 1000 1
> reference 2wc6.pdb
> rms reference out equil_0-2ns.rmsd .CA,C,N
>
> I obtain the results shown in the attached snapshot. 15+ Angstrom?
>
> Any suggestions as to the observed discrepancy would be greatly
> appreciated.
>
> Best regards
>
> George
>
>
>
>
>
>
>
>
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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 Wed Jan 04 2012 - 22:30:05 PST
