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?
By default, SPC is not intended for use with the AMBER force fields. You will
have to modify the spc.itp file to be compatible with AMBER:
http://oldwww.gromacs.org/pipermail/gmx-users/2007-June/027823.html
If grompp cannot satisfy any of the existing #ifdef statements in the [atoms]
directive, it believes that there are no water atoms, hence raising the error
when it attempts to process bonds on line 37 of spc.itp.
-Justin
Thanks,
Gunnar W.
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
