[gmx-users] How does x2top recognize between alkane C and alkene C

[sridhar dwadasi]

Hi Dr. Justin Lemkul,
      Thank you for responding again. I'm still not understanding it :(.
 I'll try to be more clear. Taking the example of OPLS UA, we have
different atom types for united alkene atoms (-CH= and CH2=) and alkanes
(-CH2-). When I represent the connections in n2t file, the -CH2- and -CH=
will have two connections each. and the distances with other united carbons
are 0.154nm and 0.140 nm as I have mentioned before. I have been giving the
same information in the .n2t file. Based on the order in which they appear
in the .n2t file, the atom appearing first is being taken by x2top to
create the topology. I hope I made my problem clear. I'm unable to post my
.n2t file now as I do not have it with me at the moment. If required I can
post it tomorrow.

Thanks and Regards
Sridhar