Hi Users:
I have a question about dummy atoms. I try to simulate a protein that have a
cysteine modified with a NO group. I found a NO model that have 3 sites, one
at each atom and other in the center of mass (Biophys. Chem. 98 (2002) 183).
[ SNC ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH2 0.00000 1
SG S 0.00000 1
ND NON -0.25000 2
CON COM 0.59500 2
OE NOO -0.34500 2
C C 0.380 3
O O -0.380 3
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
CB SG gb_30
SG ND gb_49
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
N CA C ga_12
CA C +N ga_18
CA C O ga_29
O C +N ga_32
N CA CB ga_12
C CA CB ga_12
CA CB SG ga_15
CB SG ND ga_47
SG ND OE ga_48
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
C CA +N O gi_1
CA N C CB gi_2
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
-C N CA C gd_19
N CA C +N gd_20
N CA CB SG gd_17
CA CB SG ND gd_13
CB SG ND OE gd_22
In my topology before all the bonded information I add the following lines
with the appropiate numbers:
[ dummies2 ]
;Dummy from funct a
CON ND OE 1 0.064381
[ constraint ]
; ai aj funct b0
ND OE 2 0.12032
The problem is that the dummy colapse with the ND atom during the EM. What
could be the problem? I need to add the dummies2 section in my topology if
it is present in the residue topology and it is present in my pdb???
Thanks
Anthony
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