AMBER Archive (2004)

Subject: Re: AMBER: Simulated anealling

From: anshul_at_imtech.res.in
Date: Fri Jun 04 2004 - 15:56:50 CDT

Dear Dac,
Thanks for the reply. I also thought that there may be something unusual
happening to my system, but I am afraid that I could not figure out any
such thing. I checked the rms deviation of the system (compared to the
initial one) and it is 0.34 which is not much. Since the residues from
1-167 and from 182-267 are restrained, it has a low rms deviation of about
0.2. The rmsd of all atoms in the unrestrained segment (167-181) is 2.28
It is expected that changes would occur in this region due to modifications
made in the conformation of protein. And, we are trying to analyze changes
in unrestrained region (167-182) that could possible occur after the
modifications and we want to know the behaviour of this region via
simulated anealing.
Now since it is not working well (error regarding the size of virtual box),
I would like to know how it can be simulated with AMBER 7? As you said
that there may be something BAD happening to the system, what does this
BAD actually mean? It shall be helpful if you can through some light on
the concept of this virtual box.

with regards

Anshul Awasthi
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India.
+91-9872220352

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