[gmx-users] fatal error in grompp

[Justin Lemkul]

On 7/1/16 9:14 AM, roshanak starlight wrote:
> Hello
> I'm trying to simulate the kalp-15 in dppc from gromacs Tutorial by gromacs-
> 4.5.5. When I run grompp  with this command : grompp -f minim.mdp -c
> dppc128.gro -p topol_dppc.top -o em.tpr
> I face whith this error:
>
> Fatal error:
> Syntax error - File ffnonbonded.itp, line 1
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
>
> what is the reason ?
>

You've either constructed the topology incorrectly or assembled the force field 
incorrectly.  Follow the tutorial exactly; don't skip steps or change anything 
about it.

> And an else question :is it necessary that i chang oplsaa force fileld and
> chang in lipid.itp  ?
> whit these descriptions:
>
> http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-May/021416.html
> http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-August/023587.html
> http://lists.gromacs.org/pipermail/gromacs.org_gmx-users/2006-September/023761.html
>
> I dont do it .could that fatal error is this?

That has nothing to do with your fatal error.  If you're trying to hack force 
fields, then you're not actually doing the tutorial and therefore whatever 
you're trying to do is incorrect, but you haven't really explained what you're 
doing.  Combining Berger lipid parameters with OPLS-AA does require the 
modifications that Chris describes in order to get an internally consistent 
force field description.

There are better (already consistent) force fields available, though.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================