Dear all,
My experience is that during MD alpha helix can be
changed into beta sheet.
Does any one has some experiences on the relative
movement of the domains during MD? Besides does anyone
has the experiences on conformation change from open
to closed?
I am looking forward to talking with you on these.
Best regards.
Fenghui Fan
--- Ibrahim Moustafa <I.moustafa.psu.edu> wrote:
> Thanks for Yong and Carlos for their comments.
>
> First, pardon me for not giving the details of the
> MD run in the first
> instance.
> The MD was run using AMBER9-ff99. The protein (53
> kDa, 461 aa) was solvated
> in Octa unit cell and neutralized with 6 Na+; this
> sums to a total number of
> 82,000 atoms. (This would exclude any comments
> assuming the use of GB
> model).
>
> The system was prepared by first minimization
> (alternating with Belly
> dynamics and NPT on the system being minimized),
> heating to 300 K at steps
> of 50 degrees (total 150 ps) with coupling
> "tautp=0.05", equilibrated
> further at 300 K for another 200 ps and using the
> same coupling)...these
> done using NVT model. Then the run was pursued using
> NPT for total run time
> of 5 ns (the intention is to continue the run even
> longer after analyzing
> the short 5 ns run (well, relatively speaking it is
> short by current
> computing standards).
>
> Throughout the whole run, the behaviors of TEMP,
> ENERGY, and DENISTY were
> excellent...no sign for any unusual behavior during
> the run.
>
> Then the preliminary analysis showed the sec.
> structure changes as posted
> in my previous e-mail.
>
> Looking forward to hear more from your
> experiences.
>
> Regards,
> Ibrahim
>
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of
> Yong Duan
> Sent: Wednesday, February 27, 2008 9:13 PM
> To: amber.scripps.edu
> Subject: RE: AMBER: change in secondary structure
> during MD
>
>
> All sound pretty reasonable to me :)
>
> Seriously, 5ns is not too short to see changes like
> that if they are not
> stable to begin with. Surface loops can change,
> exposed strands can also
> become loops, short helices are not very stable.
>
> The secondary structure stability (or lack of) in
> AMBER is not an inherent
> feature of AMBER, but more closely related to force
> field you are using. If
> you can let us know which force field you used and
> how you performed the
> simulations, we probably can "guess" what you see
> could be artifact of
> simulation. Treat our comments as 0th order
> approximation, though. You still
> need to investigate.
>
>
> yong
>
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of
> Ibrahim Moustafa
> Sent: Wednesday, February 27, 2008 5:45 PM
> To: amber.scripps.edu
> Subject: AMBER: change in secondary structure during
> MD
>
>
> Dear amber users,
>
> I did a 5ns MD run on a protein using AMBER9. The
> analysis of the run
> showed that, overall, the structure averaged over
> the last 500 frames is
> pretty similar to the crystal structure after the
> run, apart from meaningful
> dynamics at some parts. However, while investigating
> the structure in Pymol,
> I noticed that there is a change in some secondary
> structure elements. More
> specific: a couple of B-strands changed to loops,
> two short parts of long
> loops turned to B-strands and finally, a short helix
> turned into a loop. I
> know I do need to investigate this further by
> calculating the secondary
> structure following DSSP. But, visually I can feel
> the changes mentioned
> above.
>
> I understand that, in principle, a change in
> secondary structure could
> happen during MD, as a non-folded structure can be
> folded during simulation.
> But, I want to be sure that what I see is not an
> artifact of the simulation.
> I remember I came across some comment about the
> sensitivity of AMBER to
> B-strands stability compared to helices. Of course,
> this comment could be
> true for the previous versions of the program (I'd
> love to hear the
> developers' comments on that) which might be not the
> case for the current
> version.
>
> I'd appreciate if people with more experience could
> give me their opinions,
> and point me to publications where secondary
> structure change is reported.
>
> Thanks in advance of your help and your valuable
> comments.
>
> Regards,
> Ibrahim
>
>
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Received on Sun Mar 02 2008 - 06:07:30 PST
