AMBER Archive (2009)

Subject: [AMBER] Modification of His

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon May 18 2009 - 05:51:50 CDT

Hi all,

I am trying to modify a HIE residue in my protein which should have
different bonding properties with a metal ion. I hava taken the topology
file for HIE and made some changes to the charges of the residue making sure
it is adding to an integer. I make the following change to the HIE residue

 "ND1" "NB" 0 1 131072 9 7 -0.543200

renaming "NB" to "YB" adding the following parameters to a tmp.frcmod

MASS
YB 14.01 sp2

BOND
CC-YB 410.0 1.394
CR-YB 488.0 1.335
CV-YB 410.0 1.394

ANGLE
CT-CC-YB 70.0 120.00
CW-CC-YB 70.0 120.00
H5-CR-YB 35.0 120.00
NA-CR-YB 70.0 120.00
CC-CV-YB 70.0 120.00
H4-CV-YB 35.0 120.00
CC-YB-CR 70.0 117.00
CR-YB-CV 70.0 117.00

DIHEDRAL
X -CB-YB-X 2 5.10 180.0 2.
X -CC-YB-X 2 4.80 180.0 2.
X -CR-YB-X 2 10.00 180.0 2.
X -CV-YB-X 2 4.80 180.0 2.
CT-CW-CC-YB 1.1 180.0 2.

I start xleap by loading the topology and parameter with new modification
into xleap but it gives me this error which I thought that should be
resolved by the tmp.frcmod file
+---Tried to superimpose torsions for: *-CE1-ND1-*
+--- 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: *-CG-ND1-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes

I do not quite understand what I am doing wrongly - thanks in advance

Best regards

Jorgen
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