AMBER Archive (2006)

Subject: AMBER: problem with NAD+ parameters

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Mon Nov 06 2006 - 08:27:16 CST

Dear Amber users,

I am currently trying to attempt to do a MD simulation on a protein with NAD bound. I copied the
necessary NAD parameters available at http://pharmacy.man.ac.uk/amber/ (the frcmod.NAD+ and
NAD+.lib).

The commands I used in xleap are.

loadamberparams frcmod.nad+
loadoff NAD+.lip
prot = loadpdb prot.pdb

and i got such a message:
I: Adding /prog/AMBER9/dat/leap/prep to search path.
-I: Adding /prog/AMBER9/dat/leap/lib to search path.
-I: Adding /prog/AMBER9/dat/leap/parm to search path.
-I: Adding /prog/AMBER9/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source /prog/AMBER9/dat/leap/cmd/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

Could some one help me please? How could i solve such a problem? Does anyone have a newer
parameter files for NAD+ ?

Thanks in advance for any help.

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg
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