AMBER Archive (2008)

Subject: Re: AMBER: SPCFW problems

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Oct 28 2008 - 12:25:23 CDT

On Tue, Oct 28, 2008, Naser Alijabbari wrote:

> So I am guessing for SPCFW
>
> - WAT = SPF
>
> - set WAT.1 name 'SPF'
>
> doesn't do anything because I don't see a change in my prmtop file.

If you want the waters in the prmtop file to be named something other than
"WAT", you would have to edit the spcfwbox.off file to change the names.
(But this is likely to be more problem than it is worth: analysis programs
and so on expect waters to be named "WAT", not something else.)

What the above commands do is the following: if there are residues named
"WAT" in your input pdb file, they will be treated as SPF waters.

...dac

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