Hi:
I was running MD without problems for a protein with namd 2.9-cuda,
amber PARM7 ff (unfortunately I have no access to amber code running
cuda).
Now, I have inserted a short lipid between two aa, using GAFF params
for the lipid. Now, minimization could not be carried out: "Error: the
periodicity of dihedral #249 is zero!"
Here the relevant part of prmtop file, where the said zero is at line
3 from the bottom:
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 3.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 3.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00 3.00000000E+00
1.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 3.00000000E+00 2.00000000E+00 4.00000000E+00
3.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 4.00000000E+00 2.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 1.00000000E+00 3.00000000E+00 2.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
3.00000000E+00 4.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 4.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 4.00000000E+00 3.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00
3.00000000E+00 4.00000000E+00 3.00000000E+00 0.00000000E+00 3.00000000E+00
1.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00
I am aware that CHARMM27 uses n= 1, 2, 3, 4 in
V DA = V n [ 1 + cos (n φ2 − φ 0 )]
while I don't know if the above zero is allowed in PARM7, or if it is
an error anyway.
Frankly, I don't know from where to begin to fix the problem, and
which other data should I produce to get help.
Thanks for your understanding
francesco pietra
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Received on Tue Jul 24 2012 - 01:30:02 PDT
