AMBER Archive (2006)

Subject: Re: AMBER: problem with NAD+ parameters

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Nov 06 2006 - 16:05:52 CST

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_at_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
 
 Etiler, Ankara, 06330 Turkey
 
 Cell: +90-(536)-4813012
 
 E-Mail:cenk_andac_at_yahoo.com

 
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