Your emails are coming through. You don't need to continue sending
them. See my response to your last email.
On Thu, 2014-08-21 at 16:14 +0300, BATUHAN KAV wrote:
> 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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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 21 2014 - 06:30:07 PDT
