Dear Rodrigo,
The residue name is missing: Is it your problem?
R.E.D. Python handles many PDB file format reconstruction: in the
absence of residue name a generic one is automatically created.
More generally what do you want to get from this computation using
antechamber?
- an idea for the global conformation of this molecule? I do not think
you are going to get a representative conformation in this case.
- charge derivation? once again the conformation involved in charge
derivation will be based on... some semi-empirical algo. in gas phase,
that leads to a conformation that has nothing to do with your input
structure.
Just compare your input geometry and this sqm optimized geometry
(when/if it works).
If you want to derive charges for this molecule - instead - you could
use the building block approach implemented in R.E.D. Server, where
the nucleosides and the phosphate are present in three different
building blocks/molecules.
regards, Francois
> I am trying to run antechamber using ambertools 13 for this molecule:
>
> ATOM 1 O 1 -9.081 -2.322 -3.462
> ATOM 2 C 1 -8.756 -3.677 -3.819
> ATOM 3 C 1 -7.666 -4.201 -2.904
> ATOM 4 O 1 -6.413 -3.571 -3.239
> ATOM 5 C 1 -7.920 -3.956 -1.399
> ATOM 6 O 1 -7.696 -5.223 -0.723
> ATOM 7 C 1 -6.909 -2.874 -1.042
> ATOM 8 C 1 -5.771 -3.097 -2.040
> ATOM 9 N 1 -5.000 -1.912 -2.355
> ATOM 10 C 1 -5.455 -0.694 -2.836
> ATOM 11 N 1 -4.495 0.181 -3.049
> ATOM 12 C 1 -3.340 -0.494 -2.690
> ATOM 13 C 1 -1.977 -0.117 -2.699
> ATOM 14 N 1 -1.541 1.092 -3.096
> ATOM 15 N 1 -1.075 -1.039 -2.279
> ATOM 16 C 1 -1.497 -2.256 -1.882
> ATOM 17 N 1 -2.746 -2.724 -1.848
> ATOM 18 C 1 -3.622 -1.795 -2.262
> ATOM 19 P 1 -7.975 -5.326 0.889
> ATOM 20 O 1 -8.413 -6.749 1.185
> ATOM 21 O 1 -8.912 -4.227 1.366
> ATOM 22 O 1 -6.505 -5.025 1.545
> ATOM 23 C 1 -5.455 -5.974 1.233
> ATOM 24 C 1 -4.210 -5.630 2.023
> ATOM 25 O 1 -3.704 -4.359 1.578
> ATOM 26 C 1 -4.398 -5.547 3.564
> ATOM 27 O 1 -3.534 -6.445 4.276
> ATOM 28 C 1 -4.149 -4.066 3.869
> ATOM 29 C 1 -3.249 -3.611 2.717
> ATOM 30 N 1 -3.312 -2.194 2.397
> ATOM 31 C 1 -2.111 -1.456 2.389
> ATOM 32 O 1 -1.029 -1.944 2.713
> ATOM 33 N 1 -2.258 -0.143 2.008
> ATOM 34 C 1 -3.432 0.499 1.639
> ATOM 35 O 1 -3.421 1.699 1.302
> ATOM 36 C 1 -4.639 -0.315 1.676
> ATOM 37 C 1 -5.944 0.316 1.288
> ATOM 38 C 1 -4.513 -1.617 2.035
> ATOM 39 H 1 -2.220 1.759 -3.436
> ATOM 40 H 1 -0.528 1.282 -3.162
> ATOM 41 H 1 -0.705 -2.926 -1.546
> ATOM 42 H 1 -6.510 -0.529 -3.029
> ATOM 43 H 1 -5.039 -3.832 -1.676
> ATOM 44 H 1 -7.367 -1.894 -1.218
> ATOM 45 H 1 -6.577 -2.933 -0.003
> ATOM 46 H 1 -9.642 -4.329 -3.717
> ATOM 47 H 1 -8.391 -3.737 -4.855
> ATOM 48 H 1 -9.506 -1.908 -4.230
> ATOM 49 H 1 -7.580 -5.288 -3.063
> ATOM 50 H 1 -8.946 -3.630 -1.197
> ATOM 51 H 1 -5.788 -6.991 1.488
> ATOM 52 H 1 -5.230 -5.933 0.158
> ATOM 53 H 1 -3.466 -6.420 1.814
> ATOM 54 H 1 -5.408 -5.852 3.851
> ATOM 55 H 1 -2.616 -6.261 4.009
> ATOM 56 H 1 -5.098 -3.518 3.834
> ATOM 57 H 1 -3.692 -3.923 4.855
> ATOM 58 H 1 -2.183 -3.802 2.914
> ATOM 59 H 1 -6.767 -0.405 1.355
> ATOM 60 H 1 -5.894 0.708 0.263
> ATOM 61 H 1 -6.168 1.171 1.938
> ATOM 62 H 1 -5.363 -2.298 2.044
> ATOM 63 H 1 -1.350 0.426 1.968
> TER
>
> using this command:
>
> antechaber -i b.pdb -fi pdb -o b.mol2 -fo mol2 -c bcc -at amber -nc -1
>
> and I get the following error:
>
> Error: cannot run "/home/rodrigo/amber12/bin/sqm -O -i sqm.in -o sqm.out"
> of bcc() in charge.c properly, exit
>
> Any ideas?
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Received on Wed Sep 04 2013 - 06:00:04 PDT
