[gmx-users] Max #atoms in a charge group: 68 > 64

Samuel Coulbourn Flores 花山 scflores at stanford.edu
Mon May 26 10:50:06 CEST 2008


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
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国

















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