[AMBER] create new crd files from transformed coordinates

From: Donald Keidel <dkeidel.scripps.edu>
Date: Wed, 25 Mar 2009 01:49:03 +0000

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.scripps.edu
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm
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Received on Wed Mar 25 2009 - 01:18:46 PDT