db4 with amber5.0

From: Daniel GENEST <genest_at_cnrs-orleans.fr>
Date: Fri 23 Feb 2001 18:44:56 +0100

I used amber5.0 with db94 and parm94.dat on RNA + explicit water
+counterions. For that I have a 'PDB' file as initial conformation with
residue and atom names defined in db94.dat and parm94.dat. Now I want to
use db4.dat and parm91.dat with counterions but no water (exept a few
molecules that I think to incorporate in the topology by the ADD option of
PARM). But my 'PDB' is no more valid because the residues are not defined
in the same way in both libraries, and may be some atom names are different
too. I succeeded in performing LINK after I added CIP and CIM residues in
all.in and make db4.dat. But now I cannot perform EDIT because my 'PDB'
file does not match the file resulting from LINK. What shall I do ? Do I
have to re-write a new 'PDB' ?
Thank you for your help

* Daniel Genest * E-mail: genest_at_cnrs-orleans.fr *
* CBM - CNRS * Phone : +33 (0)2 38 25 55 93 *
* rue Charles Sadron * Fax : +33 (0)2 38 63 15 17 *
* F-45071 Orleans cedex 2 * *
Received on Fri Feb 23 2001 - 09:44:56 PST
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