Dear Rodrigo,
> 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.
The 'residue' name was missing.
We plan to first open R.E.D. Python through R.E.D. Server Dev.
sometimes this month: We are hunting and hunting bugs by now.
Using the 'whole molecule approach' in Antechamber or in R.E.D. Perl
or in R.E.D. Python will end up (I already ran R.E.D. Python on your
whole molecule using the AmberFF10 atom types & parameters) with a
non-representative conformation. It took one hour on our cluster. If
you just want to get charges for their values this is fine...
Personally, I prefer paying attention to the conformation(s) involved
in charge derivation... Thus, in your case you can easily split your
molecule into three building blocks: dimethylphosphate (DMP) +
nucleoside1 + nucleoside2. Then you define two inter-mcc
(inter-molecular charge constraints) between the target OH groups of
the nucleosides and the methyl groups of DMP and R.E.D. Perl will
perform RESP charge derivation + FF library building. R.E.D. Python
(will re-do charge derivation and) will perform atom typing + fragment
association (in your case three residues or a single one can be
requested depending on how you want to use the FF lib.) + charge
correction (no rounding off error) + frcmod generation. Many types of
extra-points can be added, etc...
A easy way to proceed until R.E.D. Python is officially available:
- run R.E.D. Server/R.E.D. IV (perl)
- write for a private assistance from the R.E.D. Server web site, and
provide the PXXXX R.E.D. Server job name.
- request post-processing of the PXXXX R.E.D. IV job using R.E.D. Python.
I can also send you how ugly is the conformation of this whole
molecule after geometry optimization using Gaussian - by 'ugly' ;-) I
mean how different from your input one (which reflects a well-designed
conformation).
regards, Francois
> 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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Received on Wed Sep 04 2013 - 09:00:02 PDT
