[gmx-users] ffnonbonded.itp and ffbonded.itp files are missing DPPC somehow

[Justin Lemkul]

On 2/12/15 11:14 PM, Thomas Lipscomb wrote:
> Dear gmx-users, I am following the KALP tutorial below:KALP-15 in DPPC
> Tutorial progress point
>
> At this step I get this error (and I know that the discrepancy is because the
> 23 DPPC molecules are not included): /usr/local/gromacs/bin/gmx grompp -f
> ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr
>
> Fatal error:number of coordinates in coordinate file (model1_solv.gro, 12266)
> does not match topology (topol.top, 11116)
>
> For more information, see my Folder with all of my KALP Tutorial files I see
> that trying to #include "dppc.itp" is not the right way to go because it has
> the same precedence as forcefield.itp. So my guess as to what is wrong is

dppc.itp and forcefield.itp are not the same precedence, and you do, in fact, 
have to #include "dppc.itp" in the system topology (this is stated in the 
tutorial and an example is given for how to do this).  The forcefield.itp file 
defines a whole force field, while dppc.itp defines a molecule within the 
context of that force field.

> that I messed up the contents of the gromos53a6_lipid.ff folder somehow when
> I was making them in "Step Two" of the tutorial. This seems to say that the
> problem is probably with these two files in the gromos53a6_lipid.ff folder:
> ffnonbonded.itp and
> ffbonded.itphttp://comments.gmane.org/gmane.science.biology.gromacs.user/50436
>
>So how do I (manually?) fix the ffnonbonded.itp and ffbonded.itp files?  Or did 
I miss a step in the tutorial?  I could redo the tutorial (up to my progress 
point) pretty quickly.

The error you've reported has nothing to do with the contents of ffbonded.itp or 
ffnonbonded.itp.  If those were faulty, you'd get grompp errors about missing 
parameters.

-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

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