load in amber99 force field in leap first.
That is,
'source leaprc.ff99'
the other leap commands of yours seem OK.
here is a couple of lines from nad+.lib
!!index array str
"NDP"
!entry.NDP.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"P1" "P" 0 1 131072 1 15 0.942647
"O1" "O2" 0 1 131072 2 8 -0.730357
"O2" "O2" 0 1 131072 3 8 -0.730357
"O3" "OS" 0 1 131072 4 8 -0.356772
..so on..
So, make sure that the residue name in prot.pdb is NDP and all NDP atom names in prot.pdb match those in nad+.lib (ie; P1, O1, O2, O3.etc) .
hope that helps,
jenk.
Urszula Uciechowska <urszula.uciechowska.pharmazie.uni-halle.de> wrote:
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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Cenk Andac, M.S., Ph.D. Student
School of Pharmacy at
Gazi University-Ankara Turkiye
Address: Bandirma Sok. No:6
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E-Mail:cenk_andac.yahoo.com
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Received on Wed Nov 08 2006 - 06:07:26 PST
