AMBER Archive (2009)

Subject: Re: [AMBER] inpcrd and prmtop

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Tue Mar 03 2009 - 03:37:16 CST

On Tue, 2009-03-03 at 09:27 +0000, m m wrote:
> Hi,
> I have built a complex and saved the prmtop and inpcrd files with
> water molecule, i forgot to save them in the gas phase, How to
> obtain the inpcrd and prmtop for the same geometry without water
> molecule.

In principle you can directly modify the two files but maybe it is
easiest to redo the procedure with leap after having removed the water
coordinates. Best would be to always store your coordinates into a PDB
file (command savepdb) which you should be able to easily load again in
leap.

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