1) Charge of the protein can be checked in tleap using "charge unit".
$ tleap
> protein=loadpdb a.pdb % first load a pdb file (a.pdb)
using the unit "protein" (You can use any unit name like mol,solute etc)
> charge protein % You can find the charge
on the unit named as protein
>addIons Na+/Cl- 0 % You can add ions according to
charge of the unit to make the system neutral (charge 0)
> charge protein %You can now check the
charge of the the unit (It should be zero if you want to make it neutral)
> quit
2) You are getting for 80ps. The extra 20ps may be your heating and
equilibration time. You may have done the heating and equilibration for
some ps which gets added to your final production run of 60 ps to give
80ps. I think you are following the tutorial B0 of the amber in which
alanine dipeptide simulation is there, in that tutorial heating of 20ps is
there. So, that gets added to 60ps production run. But, no issue, it will
always show the total time for heating, equilibration and production.
3) You just use this commad for running the script "rmsd.cpptraj"
$AMBERHOME/bin/cpptraj -p prmtop -i rmsd.cpptraj &> cpptraj.log
Then a file 02_03.rms will be made. You can open this file in the text
editor like gedit/nedit to see the time in ps and rmsd values. After
every 2ps rmsd will be written. You will get
a total of 40 frames for 80ps as you are trying to write the rmsd
after every 2ps as mentioned in the "rmsd.cpptraj" script.
On Fri, Feb 2, 2018 at 12:05 AM, Vikram Dalal <vikram.dalal.37.gmail.com>
wrote:
> Hi everyone,
> I am beginner for AMBER.
> I have tried the AMBER tutorial (
> http://ambermd.org/tutorials/basic/tutorial0/index.htm
> <https://www.researchgate.net/deref/http%3A%2F%2Fambermd.
> org%2Ftutorials%2Fbasic%2Ftutorial0%2Findex.htm>
> ).
> I have some queries:-
> 1) How can I check the charge on my protein so that I can add counter-ions
> to neutralize the system??
> 2) I have tried the MD generation. I used the following MD.in
> <https://www.researchgate.net/deref/http%3A%2F%2FMD.in>:-
> Production &cntrl imin=0, ntx=5, irest=1, nstlim=30000, dt=0.002, ntf=2,
> ntc=2, temp0=300.0, ntpr=100, ntwx=100, cut=8.0, ntb=2, ntp=1, ntt=3,
> gamma_ln=2.0, ig=-1, /
> This MD.in <https://www.researchgate.net/deref/http%3A%2F%2FMD.in> file
> shows that (30000X0.002fs= 60ps) 60ps. But i got the MD for 80 ps.
> 3) I have used following *rmsd.cpptraj*. for the RMSD generation:-
> trajin 02_Heat.mdcrd trajin 03_Prod.mdcrd reference 01_Min.rst autoimage
> rms reference mass out 02_03.rms time 2.0 :2
> I got the 800 frames in RMSD. I have to generate RMSD in terms of ps.
> How can I generate RMSD in terms of ps or ns ??
> Thank you in advance.
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 01 2018 - 21:30:02 PST
