On 7/12/12 4:59 AM, J Peterson wrote:
Hi Justin,
Thanks for the effort to help me.
I still no out of the error. The following is the content of my
topol_popc.top
; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "popc.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
; Include ion topologies
#include "gromos53a6_lipid.ff/ions.itp"
; System specifications
[ system ]
128-Lipid POPC Bilayer
[ molecules ]
; molecule name nr.
POPC 128
SOL 2460
And the following is the first part of my popc128b.gro file
Alm on surf + relaxed popc
14036
1POP C1 1 0.253 5.425 1.688
1POP C2 2 0.428 5.314 1.792
1POP C3 3 0.334 5.243 1.571
1POP N4 4 0.378 5.352 1.660
1POP C5 5 0.474 5.439 1.590
1POP C6 6 0.606 5.390 1.531
1POP O7 7 0.692 5.366 1.643
1POP P8 8 0.834 5.316 1.587
1POP O9 9 0.800 5.197 1.505
1POP O10 10 0.903 5.435 1.533
1POP O11 11 0.890 5.266 1.729
1POP C12 12 0.823 5.142 1.753
1POP C13 13 0.836 5.086 1.895
1POP O14 14 0.766 4.964 1.924
1POP C15 15 0.632 4.959 1.944
1POP O16 16 0.555 5.019 1.869
1POP C17 17 0.589 4.833 2.020
1POP C18 18 0.615 4.703 1.944
1POP C19 19 0.595 4.575 2.025
1POP C20 20 0.625 4.467 1.920
1POP C21 21 0.677 4.340 1.987
1POP C22 22 0.813 4.357 2.055
1POP C23 23 0.848 4.223 2.120
1POP C24 24 0.884 4.121 2.012
1POP C25 25 0.957 4.013 2.043
1POP C26 26 0.994 3.986 2.189
1POP C27 27 1.069 3.853 2.202
1POP C28 28 0.967 3.739 2.204
1POP C29 29 1.012 3.593 2.202
1POP C30 30 0.916 3.478 2.169
1POP C31 31 0.869 3.518 2.029
1POP C32 32 0.801 5.205 1.983
.
.
.
.
.
What are the parts mismatching in these files?
From what's shown, it's impossible to tell. Based on this information,
everything lines up. I'm assuming the original coordinate file and the popc.itp
topology came from Tieleman's site?
Since it says the atom names from the top file will be used, is it safe to
ignore this warning too?
No. The naming mismatches imply that grompp is trying to map parameters for
lipids onto water molecules. The resulting simulation will be nonsense and will
probably crash immediately.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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