AMBER Archive (2009)

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

From: Donald Keidel (dkeidel_at_scripps.edu)
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.

Don

-- 
"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 dkeidel_at_scripps.edu webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm

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