AMBER Archive (2009)

Subject: [AMBER] create new crd files from transformed coordinates

From: Donald Keidel (
Date: Tue Mar 24 2009 - 20:49:03 CDT

I have ran minimization using amber and have generated coordinates using
the -pqr option which creates a file that looks or is a pqr.

I then apply a transformation (rotation and translation) to these
coordinates and save them as another pqr. I then take the x,y, and z
coordinates and make a file that has the same format as the original
.crd file and run this new .crd file with the original .top file.

I am getting a serious error and I think amber is not happy with the new
.crd file. When I look at the 2 .crd files (original and new) I do not
see a difference. I ahve the same spacing and significant figures and
the order of the atoms is the same. Do I need to create a new .top file
that corresponds to each .crd file? I thought the .top could be used
with a transformed .crd as long as the atom order is the same.

Thank you in advance for all your help.


"The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong it usually turns out to be impossible to get at or repair."
 -- One of the laws of computers and programming revealed

Douglas Adams in "Mostly Harmless"


Donald J. Keidel, Ph.D. Research Associate The Scripps Research Institute 3377 N. Torrey Pines Court, Suite 100 La Jolla, CA 92037 mail code: TPC-26 phone: (858) 784-2842 fax: (858) 784-2341 webpage:

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