On Sat, Sep 25, 2010, hirdesh kumar wrote:
> I am trying to minimize my prepared protein in TIP3P box. I am following the
> tutorial for the sander command (
> http://ambermd.org/tutorials/advanced/tutorial8/loop5.htm). But the sander
> required the .rst file for minimization. And from my previous step of
> protein preparation using tleap I have only .parm7 and .crd files. I am
> following the simple copy conversion of protein.crd to protein.rst.
The file name per se is unimportant -- Amber doesn't use the extensions for
any purpose (unlike many other codes).
The format of the data is of course the key thing. The file that LEaP creates
is indeed of "restart" format, and can be used to begin a minimization. There
is an unfortunate fact that "crd" can be used to describe either a "restart"
file or a "trajectory" file, and those files do *not* have the same format,
and cannot be used interchangeably.
On a related point, don't be afraid to just try things when you are confused.
If you have a bad file format, you'll find out right away, and making a
mistake will not break your computer.
....dac
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Received on Sat Sep 25 2010 - 06:30:03 PDT
