[gmx-users] Error in generating DPPC using grompp

[Justin A. Lemkul]

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

-- 
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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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