[gmx-users] Max #atoms in a charge group: 68 > 64
Justin A. Lemkul
jalemkul at vt.edu
Mon May 26 14:59:00 CEST 2008
How are you generating the topology for your ligand? It would seem to me that
you'd have to do it manually, for such an odd structure, or at least use
something like PRODRG to get the initial topology. I doubt that renumbering
your molecule to make separate "residues" would solve anything. Reading in the
manual about charge groups is definitely a good idea, as well as taking a look
at similar entries (like ATP) in relevant .rtp files. This will give you some
idea about how charges are defined in similar molecules, and I know phosphates
can be especially tricky.
-Justin
Quoting Samuel Coulbourn Flores 花山 <scflores at stanford.edu>:
> So, is it generating the charge groups based on residue numbering?
> Can I solve the problem by just editing the residue number column such
> that the ligand is now composed of two "residues"? If not, how should
> I specify how the molecule is to be broken up into charge groups? How
> strict is the requirement that the charge be an integer? It seems
> unlikely that any subset of the molecule will have net integer charge.
>
> Sam
>
> ATOM 3320 PA IN4 Z 1 18.089 46.955 20.531 1.00
> 17.77 P ^M
> ATOM 3321 O1A IN4 Z 1 17.885 47.954 21.576 1.00
> 16.47 O ^M
> ATOM 3322 O2A IN4 Z 1 18.847 47.325 19.359 1.00
> 15.16 O ^M
> ATOM 3323 O3A IN4 Z 1 18.390 45.546 21.247 1.00
> 19.11 O ^M
> ATOM 3324 PB IN4 Z 1 19.799 44.954 21.708 1.00
> 16.65 P ^M
> ATOM 3325 O1B IN4 Z 1 19.334 44.008 22.760 1.00
> 15.25 O ^M
> ATOM 3326 O2B IN4 Z 1 20.626 46.063 22.136 1.00
> 17.16 O ^M
> ATOM 3327 O3B IN4 Z 1 20.354 44.137 20.429 1.00
> 15.96 O ^M
> ATOM 3328 PG IN4 Z 1 21.897 43.758 20.174 1.00
> 19.71 P ^M
> ATOM 3329 O1GAIN4 Z 1 21.897 42.507 19.181 0.50
> 18.18 O ^M
> ATOM 3330 O1GBIN4 Z 1 22.628 44.918 19.622 0.50
> 22.41 O ^M
> ATOM 3331 O2G IN4 Z 1 22.353 43.229 21.474 1.00
> 30.10 O ^M
> ATOM 3332 O3GAIN4 Z 1 22.628 44.918 19.622 0.50
> 22.41 O ^M
> ATOM 3333 O3GBIN4 Z 1 21.897 42.507 19.181 0.50
> 18.18 O ^M
> ATOM 3334 PD AIN4 Z 1 23.797 45.114 18.528 0.50
> 37.05 P ^M
> ATOM 3335 PD BIN4 Z 1 23.334 42.002 18.604 0.50
> 32.08 P ^M
> ATOM 3336 O1DAIN4 Z 1 23.854 46.581 18.294 0.50
> 43.58 O ^M
> ATOM 3337 O1DBIN4 Z 1 23.291 40.533 18.837 0.50
> 25.40 O ^M
> ATOM 3338 O2DAIN4 Z 1 23.326 44.324 17.361 0.50
> 43.58 O ^M
> ATOM 3339 O2DBIN4 Z 1 23.442 42.412 17.183 0.50
> 32.78 O ^M
> ATOM 3340 O3DAIN4 Z 1 25.870 44.772 18.892 0.50
> 36.10 O ^M
> ATOM 3341 O3DBIN4 Z 1 24.469 42.554 19.660 0.50
> 34.55 O ^M
> ATOM 3342 PE IN4 Z 1 25.829 43.456 19.553 1.00
> 25.81 P ^M
> ATOM 3343 O1EAIN4 Z 1 24.469 42.554 19.660 0.50
> 34.55 O ^M
> ATOM 3344 O1EBIN4 Z 1 25.870 44.772 18.892 0.50
> 36.10 O ^M
> ATOM 3345 O2E IN4 Z 1 26.407 43.595 20.903 1.00
> 31.63 O ^M
> ATOM 3346 O5F IN4 Z 1 16.664 46.579 19.961 1.00
> 19.72 O ^M
> ATOM 3347 C5F IN4 Z 1 16.543 45.843 18.766 1.00
> 15.12 C ^M
> ATOM 3348 C4F IN4 Z 1 15.520 46.464 17.814 1.00
> 20.75 C ^M
> ATOM 3349 O4F IN4 Z 1 14.167 46.347 18.313 1.00
> 17.34 O ^M
> ATOM 3350 C3F IN4 Z 1 15.758 47.986 17.508 1.00
> 14.48 C ^M
> ATOM 3351 O3F IN4 Z 1 15.239 48.274 16.227 1.00
> 13.13 O ^M
> ATOM 3352 C2F IN4 Z 1 14.853 48.663 18.549 1.00
> 15.06 C ^M
> ATOM 3353 O2F IN4 Z 1 14.344 49.927 18.068 1.00
> 18.78 O ^M
> ATOM 3354 C1F IN4 Z 1 13.766 47.596 18.882 1.00
> 12.64 C ^M
> ATOM 3355 N9A IN4 Z 1 13.106 47.571 20.171 1.00
> 16.08 N ^M
> ATOM 3356 C8A IN4 Z 1 13.724 47.823 21.374 1.00
> 15.47 C ^M
> ATOM 3357 N7A IN4 Z 1 12.929 47.661 22.405 1.00
> 18.45 N ^M
> ATOM 3358 C5A IN4 Z 1 11.690 47.264 21.916 1.00
> 19.01 C ^M
> ATOM 3359 C6A IN4 Z 1 10.452 46.992 22.534 1.00
> 17.84 C ^M
> ATOM 3360 N6A IN4 Z 1 10.265 47.142 23.846 1.00
> 16.43 N ^M
> ATOM 3361 N1A IN4 Z 1 9.421 46.705 21.718 1.00
> 18.69 N ^M
> ATOM 3362 C2A IN4 Z 1 9.647 46.591 20.416 1.00
> 17.51 C ^M
> ATOM 3363 N3A IN4 Z 1 10.750 46.812 19.701 1.00
> 17.03 N ^M
> ATOM 3364 C4A IN4 Z 1 11.799 47.190 20.490 1.00
> 19.52 C ^M
> ATOM 3365 O5J IN4 Z 1 26.954 42.555 18.868 1.00
> 26.97 O ^M
> ATOM 3366 C5J IN4 Z 1 27.043 42.291 17.471 1.00
> 17.15 C ^M
> ATOM 3367 C4J IN4 Z 1 28.387 41.590 17.248 1.00
> 20.83 C ^M
> ATOM 3368 O4J IN4 Z 1 29.446 42.276 17.982 1.00
> 21.77 O ^M
> ATOM 3369 C3J IN4 Z 1 28.351 40.164 17.844 1.00
> 18.19 C ^M
> ATOM 3370 O3J IN4 Z 1 27.754 39.232 16.913 1.00
> 16.22 O ^M
> ATOM 3371 C2J IN4 Z 1 29.838 39.895 18.106 1.00
> 18.14 C ^M
> ATOM 3372 O2J IN4 Z 1 30.514 39.703 16.874 1.00
> 19.73 O ^M
> ATOM 3373 C1J IN4 Z 1 30.173 41.289 18.687 1.00
> 14.80 C ^M
> ATOM 3374 N9B IN4 Z 1 30.420 41.506 20.099 1.00
> 18.44 N ^M
> ATOM 3375 C8B IN4 Z 1 29.899 42.503 20.829 1.00
> 14.07 C ^M
> ATOM 3376 N7B IN4 Z 1 30.217 42.424 22.086 1.00
> 17.74 N ^M
> ATOM 3377 C5B IN4 Z 1 30.966 41.318 22.252 1.00
> 15.06 C ^M
> ATOM 3378 C6B IN4 Z 1 31.484 40.713 23.388 1.00
> 18.26 C ^M
> ATOM 3379 N6B IN4 Z 1 31.368 41.238 24.626 1.00
> 15.83 N ^M
> ATOM 3380 N1B IN4 Z 1 32.095 39.556 23.160 1.00
> 13.73 N ^M
> ATOM 3381 C2B IN4 Z 1 32.310 39.150 21.918 1.00
> 14.83 C ^M
> ATOM 3382 N3B IN4 Z 1 31.828 39.596 20.774 1.00
> 13.67 N ^M
> ATOM 3383 C4B IN4 Z 1 31.109 40.715 20.989 1.00
> 13.30 C
>
> On May 26, 2008, at 1:16 AM, Mark Abraham wrote:
>
> > Samuel Coulbourn Flores 花山 wrote:
> >> Hi Guys,
> >> Thanks for past help received on this list.
> >> I am having a problem which I hope I can get some insight on. I am
> >> trying to simulate Adenylate Kinase binding substrate analog AP5A
> >> (from Shapiro et al). The problem is that this ligand (which is
> >> basically two Adenosines chained together with five phosphates) is
> >> a little on the large side, with 68 atoms. I get the following
> >> error on trying to run genion: Max #atoms in a charge group: 68 > 64
> >> Can someone explain to me how the ligand is different from the
> >> protein (which certainly has more than 64 atoms!)? Is the protein
> >> not considered a charge group? Can I somehow tell gromacs not
> >> treat the ligand as something other than a charge group?
> >> Alternatively, can I increase the max # atoms in a charge group?
> >> I'm happy to let it run a little more slowly if that's the only
> >> consequence.
> >
> > Look for "charge groups" in the GROMACS manual. Ideally for MD, a
> > molecule will have small groups of atoms whose total partial charge
> > is zero, and which can be lumped together in some non-bonded
> > calculations. "Small" will normally be a lot less than 64, hence the
> > constraint in genion. So probably you should go back to
> > your .top/.itp file and have a look at the [atoms] section and how
> > the charge groups are working (see table 5.3 of the manual).
> >
> > Mark
> > _______________________________________________
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>
> Samuel Coulbourn Flores
> Altman Lab
> Department of BioEngineering
> Stanford University
> samuel.flores at aya.yale.edu
> 650.644.8416
>
> 花山
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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