shobana visolingam wrote:
------------------------------------------------------------------------
dear all,
i am new to gromacs and i'm trying to run the command grompp -c
lipo1grobox.pdb -p topol.top -f em_restraints.mdp -o em_restraints.tpr.
however i got this error
*Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
ERROR 1 [file ffgmxbon_lipid.itp, line 756]:
Invalid directive DPPC
-------------------------------------------------------
Program grompp, VERSION 4.0.4
Source code file: topio.c, line: 415
Fatal error:
Syntax error - File ffgmxbon_lipid.itp, line 757
Last line read:
'[atoms]'
Invalid order for directive atoms*
can i know what this error mean and how to overcome it?? thanks.
You have serious errors in your topology. Without seeing it, there's nothing
else anyone can really suggest except for having a thorough read through Chapter
5. The topology must follow a specific order, which you likely have not
followed. A simple DPPC topology is available as part of my membrane protein
tutorial:
http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations
-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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