AMBER Archive (2006)

Subject: AMBER: NAD parameters

From: alexandra.marques_at_fc.up.pt
Date: Mon Jan 30 2006 - 10:04:43 CST

Dear Amber users,

I used the parameters files for NAD+ available at
http://pharmacy.man.ac.uk/amber/ (those produced by Walker et al.). However
when I load them in xleap together with the pdb file that I am interested a
weird message appears in the terminal:

-I: Adding /scratch/programs/amber8//dat/leap/prep to search path.
-I: Adding /scratch/programs/amber8//dat/leap/lib to search path.
-I: Adding /scratch/programs/amber8//dat/leap/parm to search path.
-I: Adding /scratch/programs/amber8//dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leaprc.ff99.
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C18-N7-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C21-N6-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C16-N6-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C15-N6-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes

The commands I used in xleap are:

mods = loadamberparams nad.frcmod
loadoff nad.off
x = loadpdb protein.pdb

and the message above appears precisely after I load the pdb file
containing the
protein.
Could someone help me please me? Does anyone know if there is newer parameter
files for NAD+?

Best regards
Alexandra

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