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error in tutorial(Soluble protein-ubiquitin)
- wangxy
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8 years 9 months ago - 8 years 9 months ago #4685
by wangxy
error in tutorial(Soluble protein-ubiquitin) was created by wangxy
in section "Soluble protein: the Martini description", the ubiquitin,
After step 5,
$ genbox -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -vdwd 0.21 -o system-solvated.gro
I got 1663 coordinates, seen in the 1st 2 lines of "system-solvated.gro". Then in step 6, I used the tutorial offered "system.top", typed in command
$ grompp -f minimization.mdp -c system-solvated.gro -p system.top -o minimization.tpr
and got the message:
"
Fatal error:
number of coordinates in coordinate file (system-solvated.gro, 1663)
does not match topology (system.top, 906)
"
so I looked in "system.top":
"
[ molecules ]
; name number
Protein_A 1
W 743
"
the number of waters really doesn't match.
If I modify "W 743" to "W 1500", it might work. But the result will differ from the tutorial package.
So the question is what should I do to continue the tutorial and get the same results as in the package?
I tried cut the last lines in the .gro file, but the box was ruined.
my gromacs version 4.6.7
After step 5,
$ genbox -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -vdwd 0.21 -o system-solvated.gro
I got 1663 coordinates, seen in the 1st 2 lines of "system-solvated.gro". Then in step 6, I used the tutorial offered "system.top", typed in command
$ grompp -f minimization.mdp -c system-solvated.gro -p system.top -o minimization.tpr
and got the message:
"
Fatal error:
number of coordinates in coordinate file (system-solvated.gro, 1663)
does not match topology (system.top, 906)
"
so I looked in "system.top":
"
[ molecules ]
; name number
Protein_A 1
W 743
"
the number of waters really doesn't match.
If I modify "W 743" to "W 1500", it might work. But the result will differ from the tutorial package.
So the question is what should I do to continue the tutorial and get the same results as in the package?
I tried cut the last lines in the .gro file, but the box was ruined.
my gromacs version 4.6.7
Last edit: 8 years 9 months ago by wangxy.
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