AMBER Archive (2005)

Subject: Re: AMBER: How to modify force constants and equalibrium values for standard residues

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 16 2005 - 09:41:18 CDT

On Thu, Jun 16, 2005, Li Su wrote:
>
> I'm wondering if there is someway for me to modify force constants and
> equalibrium values for standard residues besides directly change the prmtop
> file. If it is the only way (the amber script I'm using is installed on
> some mainframe,so I can't modify it' s library), where can I find some
> straightforward examples? Thank you in advance.

You can create a "frcmod" file that modifies the parameters found in the
standard library. Examples of this are in tutorials 4 and 5 of the "PSC 2005
workshop" tutorials at the Amber web page.

Alternatively, you can make a local copy of the installed parm94.dat file (or
whichever file you have been using), modify it, and load that instead of the
standard file, using the loadAmberParams command in LEaP.

The advantage of the frcmod approach is that you have a nice record of exactly
what was changed. But either way should work.

...dac

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