Hi Alan,
Hmm, those are NMR structures with lots of choices as to which ATP to
use. I tried both model 1 and model 14 from 1JKN and sqm failed for
both using default criteria. I didn't try any of 2B6F since the ATP
is covalently bound to a glycine in that entry. I don't suppose you
remember which particular model of 1JKN you used that converged?
--Eric
On Mar 19, 2010, at 9:34 AM, Alan wrote:
> I once used the ATP from 2B6F and 1JKN and it seemed to work for me
> with -4
> net charge.
>
> It's all about the initial structure of your molecule.
>
> Alan
>
> On Fri, Mar 19, 2010 at 00:17, Eric Pettersen <pett.cgl.ucsf.edu>
> wrote:
>
>> I'll just cut and paste the sqm.in file, since it's short:
>>
>> Run semi-empirical minimization
>> &qmmm
>> qm_theory='AM1', grms_tol=0.02,
>> tight_p_conv=0, scfconv=1.d-7, qmcharge=-4,
>> /
>> 15 PG 7.7270 -127.7270 -164.2590
>> 8 O1G 7.1390 -129.0740 -164.0840
>> 8 O2G 7.1960 -126.6730 -163.1630
>> 8 O3G 7.3760 -127.1060 -165.6990
>> 15 PB 10.1260 -126.3960 -164.6610
>> 8 O1B 9.4570 -125.1840 -164.1420
>> 8 O2B 10.2690 -126.5480 -166.1250
>> 8 O3B 9.3310 -127.6920 -164.1370
>> 15 PA 11.7330 -126.4560 -162.3570
>> 8 O1A 12.3780 -125.1570 -162.0590
>> 8 O2A 10.4420 -126.7610 -161.7010
>> 8 O3A 11.5660 -126.5470 -163.9550
>> 8 O5' 12.7770 -127.6400 -162.0360
>> 6 C5' 13.0970 -128.6550 -162.9930
>> 6 C4' 13.0520 -130.0350 -162.3350
>> 8 O4' 13.7310 -131.0510 -163.0970
>> 6 C3' 13.7730 -129.9820 -160.9880
>> 8 O3' 12.8470 -129.5630 -159.9830
>> 6 C2' 14.0860 -131.4660 -160.8180
>> 8 O2' 12.8750 -132.1970 -160.6110
>> 6 C1' 14.6320 -131.7500 -162.2180
>> 7 N9 16.0030 -131.1990 -162.3840
>> 6 C8 16.3250 -129.9360 -162.6610
>> 7 N7 17.6490 -129.8280 -162.7800
>> 6 C5 18.1790 -131.0310 -162.5780
>> 6 C6 19.4730 -131.5300 -162.6070
>> 7 N6 20.5090 -130.7300 -162.8610
>> 7 N1 19.6790 -132.8970 -162.3780
>> 6 C2 18.5740 -133.7230 -162.1230
>> 7 N3 17.3560 -133.2130 -162.1020
>> 6 C4 17.1230 -131.9070 -162.3210
>> 1 H5' 14.0980 -128.4760 -163.3860
>> 1 H5'' 12.3770 -128.6210 -163.8100
>> 1 H4' 12.0140 -130.3300 -162.1800
>> 1 H3' 14.6710 -129.3640 -161.0160
>> 1 HO3' 13.2910 -129.5270 -159.1330
>> 1 H2' 14.8240 -131.6500 -160.0370
>> 1 HO2' 13.0310 -132.9030 -159.9790
>> 1 H1' 14.6200 -132.8200 -162.4260
>> 1 H8 15.6210 -129.1240 -162.7720
>> 1 H61 20.3580 -129.7460 -163.0310
>> 1 H62 21.4450 -131.1080 -162.8840
>> 1 H2 18.7200 -134.7780 -161.9440
>>
>>
>> On Mar 18, 2010, at 5:11 PM, Eric Pettersen wrote:
>>
>> Hmm, I don't see the attachments that were in the mail I sent. Is
>> there
>>> some magic to avoid having them stripped?
>>>
>>> --Eric
>>>
>>> On Mar 18, 2010, at 5:07 PM, Eric Pettersen wrote:
>>>
>>> Hi,
>>>> I cannot get sqm to produce SCF convergence for an ATP
>>>> derived
>>>> from PDB 1xfa, even with the convergence criteria cranked way
>>>> down. Is it
>>>> because of the high charge (-4)? Is there anything that can be
>>>> done to get
>>>> it to converge? I've attached the sqm.in file (with the lowered
>>>> criteria), sqm.out file, and the mol2 file that was fed to
>>>> Antechamber
>>>> originally. The sqm command line I used was the same as
>>>> antechamber uses:
>>>> sqm -O -i sqm.in -o sqm.out.
>>>>
>>>> --Eric
>>>>
>>>> Eric Pettersen
>>>> UCSF Computer Graphics Lab
>>>> http://www.cgl.ucsf.edu
>>>>
>>>>
>>>>
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>>
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>
>
>
> --
> Alan Wilter Sousa da Silva, D.Sc.
> PDBe group, PiMS project http://www.pims-lims.org/
> EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10
> 1SD, UK
> +44 (0)1223 492 583 (office)
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Received on Fri Mar 19 2010 - 10:00:04 PDT
