[AMBER] Problem with cpptraj autoimage command

From: Karolina Markowska <markowska.kar.gmail.com>
Date: Thu, 6 Aug 2015 13:35:59 +0200

Dear Amber Users,

I have a problem with cpptraj and it's autoimage command. My system
consists of two chains and two Mn2+ ions. I usually use the script below,
but when I use it on this system, something went wrong.

reference protein_complex.inpcrd
trajin emd2.traj.gz
center :1-374 mass origin
image origin center
rms ToRef :1-374.CA,C,N= reference out rmsd_prod.arg mass
atomicfluct out rmsf_prod.arg :1-374 byres
trajout protein_complex_f.binpos binpos

I looks like only the first chain was centered. I've tried to change the
autoimage command and put:

autoimage anchor :1-374

because I've read in the Amber Manual, that autoimage by default center
only the first molecule, but after that the water box looked wierd.

The problem is with the autoimage command or with something else?
What should I do to have two chains of my system centered in the water box
(truncated octahedron shape)?

Best regards,
Karolina Markowska
PhD student
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Received on Thu Aug 06 2015 - 05:00:04 PDT
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