Hello
My A.gro file is:
1PvB CB 1 3.109 2.784 0.803 0.0000 0.0000 0.0000
1PvB HB1 2 3.156 2.880 0.843 0.0000 0.0000 0.0000
1PvB HB2 3 2.997 2.797 0.819 0.0000 0.0000 0.0000
1PvB HB3 4 3.129 2.765 0.693 0.0000 0.0000 0.0000
1PvB CA 5 3.173 2.673 0.879 0.0000 0.0000 0.0000
........... (contd.)
My ffbonded.itp file has:
[ bondtypes ]
; i j func b0(bond length) kb (force const)
CB HB1 1 0.11 284512
CB HB2 1 0.11 284512
CB HB3 1 0.11 284512.0
... (contd)
[ angletypes ]
; i j k func th0 cth
HO OH CA 1 105 320
CA CB CA 1 109.45 482.3
CB CA CB 1 109.45 482.3
OH CA CB 1 107.8 460
....... (contd)
[ dihedraltypes ]
; i j k l func RB coefficients
OH OH CA CB 3 3.00000 9.00000 0.00000 -12.00000
0.00000 0.0000 ;
CA CB CA CB 3 5.75000 17.25000 0.00000 -23.00000
0.00000 0.0000 ;
..... (contd)
However, my topol.top file looks like this:
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
1 12 1
........(contd)
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 1
2 1 4 1
2 1 5 1
2 1 12 1
3 1 4 1
3 1 5 1
......... (contd)
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
2 1 5 6 3
2 1 5 7 3
3 1 5 6 3
3 1 5 7 3
4 1 5 6 3
4 1 5 7 3
....... (contd)
I have two issues:
1) I have mentioned the bond lengths and bond constants in the [bondtypes]
and [angletypes ]directory of the ffbonded.itp file, however in the [bonds]
[ angles ]directory in the topol.top file the Ryckaert-Bellemans
coefficients are used, which are assigned as blanks. This is giving the
error No default Ryckaert-Bell. types (multiple times).
2) Also, the RB coefficients mentioned in the [dihedraltypes] of the
ffbonded.itp are not used in the [dihedrals] directory of the topol.top
file. This is again writing blanks for the RB coefficients.
What is the issue and why is my topl.top file inconsistent with the inputs
given in the ffbonded.itp file?
Thank You
Sreeta
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