Dear All,
I am trying to parametrize desoxycorticosterone (C_21-H_30-O_3) with
antechamber. Then I will simulate this molecule along with the protein.
Using antechamber, I entered this command
antechamber -i des.pdb -fi pdb -o des.mol2 -fo mol2 -c bcc -s 2
but I ended up with
Error: cannot run "/home/peptid/Desktop/master/software/amber14/bin/sqm -O
-i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
and tail of sqm.out file is
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.4929E+06 DeltaE = 0.1319E+01 DeltaP = 0.4179E-01
QMMM: Smallest DeltaE = 0.2006E-04 DeltaP = 0.2178E-02 Step = 94
Below is the pdb file I used for the ligand.
HETATM 2068 C1 1CA A 247 -9.669 -30.195 -21.851 1.00
26.17 C
HETATM 2069 C2 1CA A 247 -10.143 -29.383 -23.056 1.00
26.85 C
HETATM 2070 C3 1CA A 247 -11.556 -28.862 -22.800 1.00
29.65 C
HETATM 2071 C4 1CA A 247 -11.956 -28.557 -21.504 1.00
27.46 C
HETATM 2072 C5 1CA A 247 -11.112 -28.734 -20.413 1.00
25.76 C
HETATM 2073 C6 1CA A 247 -11.623 -28.332 -19.028 1.00
24.16 C
HETATM 2074 C7 1CA A 247 -11.259 -29.375 -17.972 1.00
22.80 C
HETATM 2075 C8 1CA A 247 -9.773 -29.730 -18.038 1.00
23.73 C
HETATM 2076 C9 1CA A 247 -9.464 -30.354 -19.402 1.00
24.99 C
HETATM 2077 C10 1CA A 247 -9.733 -29.384 -20.556 1.00
24.39 C
HETATM 2078 C11 1CA A 247 -8.037 -30.910 -19.462 1.00
24.90 C
HETATM 2079 C12 1CA A 247 -7.778 -31.925 -18.345 1.00
23.64 C
HETATM 2080 C13 1CA A 247 -8.036 -31.258 -16.993 1.00
25.19 C
HETATM 2081 C14 1CA A 247 -9.482 -30.769 -16.954 1.00
24.25 C
HETATM 2082 C15 1CA A 247 -9.581 -30.263 -15.515 1.00
25.28 C
HETATM 2083 C16 1CA A 247 -8.860 -31.367 -14.735 1.00
28.25 C
HETATM 2084 C17 1CA A 247 -8.148 -32.209 -15.799 1.00
26.28 C
HETATM 2085 C18 1CA A 247 -7.052 -30.116 -16.731 1.00
19.48 C
HETATM 2086 C19 1CA A 247 -8.681 -28.273 -20.568 1.00
22.66 C
HETATM 2087 C20 1CA A 247 -6.788 -32.689 -15.290 1.00
26.82 C
HETATM 2088 C21 1CA A 247 -6.080 -33.822 -16.038 1.00
25.81 C
HETATM 2089 O3 1CA A 247 -12.349 -28.746 -23.733 1.00
32.88 O
HETATM 2090 O20 1CA A 247 -6.289 -32.178 -14.289 1.00
28.16 O
HETATM 2091 O21 1CA A 247 -4.729 -33.980 -15.601 1.00
26.05 O
I am not sure what to do next with the above error. Any help would be
greatly appreciated.
Cheers,
Batuhan
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Received on Thu Aug 21 2014 - 06:30:06 PDT
