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