Gunnar Widtfeldt Reginsson wrote:
I am trying to run grompp using a pdb file of DNA duplex, a sucessfully
generated topology, and the steep.mpd
from http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top
I am getting the fatal error:
Fatal error:
[ file spc.itp, line 37 ]:
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology section "bonds"
in a part belonging to a different molecule than you intended to.
In that case move the "bonds" section to the right molecule.
I am using the amber99 force field, and have followed the notes on
nucleic acids on http://chemistry.csulb.edu/ffamber/
I am new to Gromacs, can anyone help me with this?
Their website example .top uses amber_tip4p water, while their website
pdb2gmx instructions won't replicate this. Please take that up with them.
Your inclusion of spc.itp is probably in the wrong place. You need all [
moleculetypes ] before [ system ] and [ molecules ] and all parts of a [
moleculetype ] need to follow each other directly. See example in
chapter 5 of the manual.
Mark
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