Hi all,
I am trying to model in NH4+ residues so I created the following toph and param
files:
REMARKS TOPOLOGY FILE AMMONIUM
REMARKS ======================
SET ECHO=FALSE END
AUTOGENERATE ANGLES=TRUE END
! ---------------------------------------------------------------------
MASS NH 14.0067 !nitrogen
MASS HN 1.0080
! ---------------------------------------------------------------------
RESIdue NH4 { NH4 }
GROUp
ATOM NH TYPE NH CHARGE 0.0 END
ATOM HN1 TYPE HN CHARGE 0.25 END
ATOM HN2 TYPE HN CHARGE 0.25 END
ATOM HN3 TYPE HN CHARGE 0.25 END
ATOM HN4 TYPE HN CHARGE 0.25 END
BOND NH HN1
BOND NH HN2
BOND NH HN3
BOND NH HN4
END { NH4 }
================================================================================================================================================================
REMARKS PARAMETER FILE FOR AMMONIUM MOLECULE AND SOLVENT INTERACTIONS
BOND HN NH 370.0 1.034
ANGLE HN NH HN 40.0 109.5
{ POTENTIAL FOR NONBONDED INTERACTIONS }
! eps sigma eps(1:4) sigma(1:4)
! (kcal/mol) (A)
! ---------------------------------------
NONBonded NH 0.2384 2.8509 0.2384 2.8509
NONBonded HN 0.0498 1.4254 0.0498 1.4254
================================================================================================================================================================
But when I run xplor and try H-build I get the following message in the *.out
file and the following *.pdb file
HBUILD: dihedral PHI STePs for spin = 4.0000
HBUILD: cutoff during water acceptor search = 7.5000
HBUILD:HN1 ,HN2 ,HN3 ,HN4 placed for water 2001 NH4 NH .
HBUILD:HN1 ,HN2 ,HN3 ,HN4 placed for water 2002 NH4 NH .
HBUILD:HN1 ,HN2 ,HN3 ,HN4 placed for water 2003 NH4 NH .
REMARK FILENAME="plc_NH4.pdb"
REMARK PARAMETER FILE FOR AMMONIUM MOLECULE AND SOLVENT INTERACTIONS
REMARK DATE:12-04 -95 21:52:25 created by user:
ATOM 1 NH NH4 2001 24.528 15.339 -0.849 1.00 65.22
ATOM 2 HN1 NH4 2001 24.528 16.373 -0.849 1.00 0.00
ATOM 3 HN2 NH4 2001 24.528 14.994 -1.824 1.00 0.00
ATOM 4 HN3 NH4 2001 999.000999.000 999.000 1.00 0.00
ATOM 5 HN4 NH4 2001 999.000999.000 999.000 1.00 0.00
ATOM 6 NH NH4 2002 25.847 21.814 -0.056 1.00 20.00
ATOM 7 HN1 NH4 2002 25.847 22.848 -0.056 1.00 0.00
ATOM 8 HN2 NH4 2002 25.847 21.469 -1.031 1.00 0.00
ATOM 9 HN3 NH4 2002 999.000999.000 999.000 1.00 0.00
ATOM 10 HN4 NH4 2002 999.000999.000 999.000 1.00 0.00
ATOM 11 NH NH4 2003 21.924 20.669 1.071 1.00 38.73
ATOM 12 HN1 NH4 2003 21.924 21.703 1.071 1.00 0.00
ATOM 13 HN2 NH4 2003 21.924 20.324 0.096 1.00 0.00
ATOM 14 HN3 NH4 2003 999.000999.000 999.000 1.00 0.00
ATOM 15 HN4 NH4 2003 999.000999.000 999.000 1.00 0.00
END
It appears that XPLOR is viewing my nitrogen of NH4+ as a water and is only
giving coordinates for two of the hydrogens in NH4+ and doesnot know what
coordinates to give the other two hydrogens coordinates.
What am I doing wrong here?
How do I get XPLOR to put in coordinates for all 4 hydrogens in NH4+?
Did I do something wrong in setting up my toph and param files?
Did I forget to put something into my toph and param files?
Any help would greatly be appreciated!
Thanks in advance!
--
Robert D Scavetta
Dr. Francis Jurnak's Laboratory
Department of Biochemistry
University of California, Riverside
scavetta at xtreme.ucr.edu or scavetta at ucrac1.ucr.edu
