Thank you Fracois.
I want to obtain the charge of each atom to perform a minimization of the
structure. You are right the name of the molecule was missing. I didn't
know about RED python I will give it a try.
2013/9/4 FyD <fyd.q4md-forcefieldtools.org>
> 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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--
Atentamente
Rodrigo Salazar
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Received on Wed Sep 04 2013 - 08:00:04 PDT
