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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Received on Thu Feb 01 2018 - 11:00:02 PST
