AMBER Archive (2006)

Subject: AMBER: Ptraj syntax change Amber8->Amber9 ?

From: Markus Kaukonen (
Date: Wed Nov 22 2006 - 04:35:26 CST

Dear Matrix,

I use ptraj to move water molecules close to the protein (here residues
Ptraj command I use is:
image center byres :WAT familiar com :1-217

This is fine with Amber8 but not with Amber9.

With Amber9 one gets a warning:
WARNING: Error in mask string, no "@" or ":" present (byres)
and no water molecules are moved

Additionally a wish. Could the section in the manual Ptraj/Image (Pages
252-253 of Amber9 pdf manual) be rewritten with more examples?
As it stands now I can't understand much of it.

Terveisin, Markus

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