On 6/29/12 3:55 PM, sreeta.g wrote:
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).
The "blanks" in the topology are totally normal. When assembling the .tpr file,
grompp will look up the appropriate values in ffbonded.itp that match with the
atom types it finds. If you are getting errors about missing parameters, you
have failed to assign some interaction type. The error message should contain
the offending lines. Note, too, that the parameters specified in ffbonded.itp
are assigned by atom *type* and not atom *name* - perhaps this is the origin of
your problem.
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?
The blanks are normal; see above comments.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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