AMBER Archive (2009)

Subject: Re: [AMBER] inpcrd and prmtop

From: Gustavo Seabra (
Date: Tue Mar 03 2009 - 14:20:38 CST

On Tue, Mar 3, 2009 at 4:27 AM, 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.
> Thanks

There's really no way to do what you want from the prmtop/inpcrd files
directly from LEaP. As François mentioned, you can probably do that
using the "rdparm" program (from AmberTools) and the "stripwater"
command. Look into the AmberTools manual, the "ptraj" session.

Apparently, creating those files was quite some work from you,
otherwise you would not be looking for this option ;-) If you still
have the old leap.log file, you can just strip the outputs from LEaP
and use the file as a LEaP script to recreate the molecule the way you

Good luck,

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