Mark Abraham wrote:
; water topology
#include "tip3p.itp"
grompp is not detecting the change of [moleculetype], so you will have
to look at the contents of that tip3p.itp and see why. I think you will
need to #include some standard force field to get the water parameters.
Put the #include for tip3p.itp above your [moleculetype] to get some
different diagnostics that may be more helpful.
I think the problem is due to the fact that tip3p.itp in $GMXLIB does not
#include the proper file in the Amber directory. The series of #ifdefs (none of
which can be satisfied in this topology, anyway) cover only Gromos and OPLS.
Try #include "amber03.ff/tip3p.itp" or something similar for whichever Amber
force field you want to use.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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