[gmx-users] Re: x2top

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 23 14:03:14 CET 2010

Vitaly V. Chaban wrote:
> Try to use the following:
> x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -pbc

The -pbc option (in version 4.0.x) causes the program to hang.  You have to use 
-nopbc, even if the molecule is "infinite."  You'll have to fix the topology 
later.  To use OPLS, the .n2t file will have to be modified to include the 
appropriate Si-O connectivities which are not present by default.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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