AMBER Archive (2008)

Subject: Re: AMBER: Read trajectories generated by CHARMM

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 28 2008 - 10:25:13 CDT

On Mon, Apr 28, 2008, Jeffrey wrote:
>
> I noticed that by setting ismem=1 in AMBER, the memory requirement can
> be reduced to 1/3, which can be fulfilled by our machines.
> So I want to know whether AMBER can read the trajectories generated by CHARMM?
Normal mode caculations use the ismem parameter, which require you to minimize
a structure first. You could use ptraj to read a CHARMM trajectory, convert
it to Amber restart format, and give those snapshots to nmode.

> If so, which forcefield should I use?

It would be better to download AmberTools and use NAB (with a GB forcefield)
to carry out the normal mode analysis. Of course, mixing a CHARMM-generated
trajectory (with its forcefields) and an Amber analysis (with different force
fields) is likely to create data that is difficutl to interpret. Is there a
reason why you don't want to do the normal mode analysis in CHARMM?

...dac

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