AMBER Archive (2007)

Subject: AMBER: General AMBER questions

From: Lili Peng (lilipeng_at_gmail.com)
Date: Tue Jul 17 2007 - 17:51:32 CDT

Dear all,

I have some basic questions on AMBER v9 that have come up while using it.
These are probably very basic questions, so if they've been asked before,
sorry for the repeat.

1. How do we extract a file of the output data? I have Googled this
problem, and I came up with "ambpdb" and "ptraj" - is this the right
direction?

2. How do we determine force constants for restraint groups in Sander?

3. Is there a way to determine the timescale for an energy minimization run?

4. From reading literature, I've noticed that a lot of authors use RES to
calculate RESP charges for molecules. Is it always necessary to do this
prior to an MD simulation, or energy minimization?

Again, thank you for your time. I appreciate it.

Regards,
Lili

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