exclusions.dat

The file format for describing exclusions between all interaction sites of the system. This file is created by [rdf]rdf.py and used a input to [magic]MagiC core. It can be edited manually if necessary.

The first two lines of the file state exclusion rules for each molecular type of the system, i.e. define the maximum number of bonds between atoms which is enough to exclude them from the non-bonded interactions. All remaining lines specify site-site exclusions:
<site number> : <list of sites which do not have NB interactions to the given site> Example of exclusion file for DMPC-Cholesterol mixture:

NAngleBondsExclude=Chol.CG:1,DMPC.CG:1
NPairBondsExclude=Chol.CG:-1,DMPC.CG:1
1:2,3,4
2:1,3,4,5,8
3:1,2,4,5,6,8
4:1,2,3,5,8,9
5:2,3,4,6,7
6:3,5,7
7:5,6
8:2,3,4,9,10
9:4,8,10
10:8,9
11:12,13,14,15
12:11,13,14,15
13:11,12,14,15
14:11,12,13,15
15:11,12,13,14

The last five lines of this example imply that therer are no non-bonded interaction within coarse-grained cholesterol molecule defined by sites 11-15.