Dear Gromacs users,
I am trying to simulate an "infinite" protein chain by covalently bonding
the last residue of my structure to the first residue across the periodic
boundary. I have modified the topology file to include these bonded
interactions and have specified "periodic-molecules=yes" in my mdp file.
However, when attempting to use grompp, I get many errors of the type "No
default Bond types" "No default U-B types" etc.
Below is a snippet of the first residue of my structure:
0ALA N 1 -2.130 11.857 5.885
0ALA HN 2 -2.194 11.930 5.907
0ALA CA 3 -2.193 11.725 5.916
And a snippet of the last residue:
179THR HG23 2660 3.379 11.851 6.387
179THR C 2661 3.583 11.711 6.162
179THR O 2662 3.514 11.783 6.087
I have identified and added ~30 bonded interactions to my topology file.
For example, the carbon in THR should be bonded to the nitrogen in ALA, so
I have added the following line (line #5541 in my .top file):
[ bonds ]
; ai aj funct c0 c1 c2 c3
2661 1 1
However, grompp returns the following error:
ERROR 1 [file monomer_3.top, line 5541]:
No default Bond types
Similar errors are produced for most (but not all) of the added
interactions. All of the "pairs" and four of the "dihedrals" were processed
without errors. I cannot find a pattern in the dysfunctional vs functional
lines. For example, the following dihedral did not return an error:
(179THR N 2649 )-(179THR CA 2651 )-(179THR C 2661 )-(0ALA
N 1 )
However, this dihedral did:
(179THR CA 2651 )-(179THR C 2661 )-(0ALA N 1 )-(0ALA
HN 2 )
Any help in debugging this would be much appreciated!
Thanks in advance,
Rachel Baarda
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