Re: [AMBER] Fit the trajectory to the original inpcrd file

From: Daniel Roe <>
Date: Fri, 6 Jul 2018 09:26:51 -0400

You can use cpptraj to do this. Please note that you have to rms-fit
*before* you image - once you rotate your coordinates they will no
longer align with the original unit cell vectors making imaging
impossible. The following input is an example:

parm myparm.parm7
reference original.inpcrd
# This mask selects all non-water atoms. You may need to
# adjust it for your particular system.
rms reference !:WAT

Hope this helps,


On Fri, Jul 6, 2018 at 8:40 AM, Meng Wu <> wrote:
> Dear all,
> Just a quick question, is there any way to fit my trajectory to the original inpcrd file and then image it? Please give me more detailed help as much as possible, thank you very much!
> All the best,
> Vector
> _______________________________________________
> AMBER mailing list

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Received on Fri Jul 06 2018 - 06:30:03 PDT
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