[gmx-users] Removing errors related to missing dihedrals.

Abhishek Acharya aacharya at iitk.ac.in
Tue Feb 12 12:19:50 CET 2013


Hello Justin.
Help would really be appreciated. And yes you are correct and i
thought the same. Initially I tried using opls_345B but it didn't
work. In fact if I use opls_345B it gives me an additional error.
Anyhow here are the relevant files.
topology file:
 #   [atoms]
15  ;   nr       type  resnr residue  atom   cgnr     charge
mass  typeB    chargeB      massB
16       1   opls_445      1    GDP      P      0      1.2596
30.97376
17       2   opls_446      1    GDP     O2      0     -0.9034
15.99940
18       3   opls_446      1    GDP     O2      0     -0.9070
15.99940
19       4   opls_446      1    GDP     O2      0     -0.9275
15.99940
20       5   opls_441      1    GDP     O2      0     -0.5156
15.99940
21       6   opls_440      1    GDP      P      0      1.2391
30.97376
22       7   opls_441      1    GDP     O2      0     -0.8867
15.99940
23       8   opls_441      1    GDP     O2      0     -0.8450
15.99940
24       9   opls_442      1    GDP     OS      0      0.4846
15.99940
25      10   opls_443      1    GDP     CT      1      0.0706
12.01100
26      11   opls_140      1    GDP     HC      1      0.0827
1.00800
27      12   opls_140      1    GDP     HC      1      0.0827
1.00800
28      13   opls_183      1    GDP     CT      2      0.0348
12.01100
29      14   opls_185      1    GDP     HC      2      0.0538
1.00800
30      15   opls_180      1    GDP     OS      2     -0.4621
15.99940
31      16   opls_158      1    GDP     CT      3      0.2388
12.01100
32      17   opls_156      1    GDP     HC      3      0.1674
1.00800
33      18   opls_154      1    GDP     OH      3     -0.7755
15.99940
34      19   opls_155      1    GDP     HO      3      0.4336
1.00800
35      20   opls_158      1    GDP     CT      4      0.2713
12.01100
36      21   opls_156      1    GDP     HC      4      0.0890
1.00800
37      22   opls_154      1    GDP     OH      4     -0.7534
15.99940
38      23   opls_155      1    GDP     HO      4      0.4404
1.00800
39      24   opls_137      1    GDP     CT      5     -0.0774
12.01100
40      25   opls_140      1    GDP     HC      5      0.0594
1.00800
41      26   opls_354      1    GDP     NA      6      0.1656
14.00670
42      27   opls_353      1    GDP     CK      7      0.1470
12.01100
43      28   opls_359      1    GDP     H5      7      0.2255
1.00800
44      29   opls_352      1    GDP     NB      8     -0.5913
14.00670
45      30   opls_365      1    GDP     CB      9      0.1189
12.01100
46      31   opls_366      1    GDP      C     10      0.5578
12.01100
47      32   opls_370      1    GDP      O     10     -0.6203   14.00670
48      33   opls_361      1    GDP     NA     11     -0.5509
14.00670
49      34   opls_367      1    GDP      H     11      0.3354
1.00800
50      35   opls_362      1    GDP     CA     12      0.7061
12.01100
51      36   opls_368      1    GDP     N2     13     -0.9532
14.00670
52      37   opls_369      1    GDP      H     13      0.3790
1.00800
53      38   opls_369      1    GDP      H     13      0.3790
1.00800
54      39   opls_363      1    GDP     NC     14     -0.5526
14.00670
55      40   opls_364      1    GDP     CB     15      0.1142   12.01100

225 [ dihedrals ]
226 ;  ai    aj    ak    al funct
227    25    24    26    27     3
228    25    24    26    40     3
229    24    26    27    28     3
230    24    26    27    29     3
231    36    35    39    40     3
232    21    20    22    23     3
233    21    20    24    25     3
234    21    20    24    26     3
235    22    20    24    25     3
236    22    20    24    26     3
237    18    16    20    21     3
238    18    16    20    22     3
239    18    16    20    24     3
240    17    16    20    21     3
241    17    16    20    22     3
242    17    16    20    24     3
243    14    13    15    24     3
244    14    13    16    18     3
245    14    13    16    17     3
246    14    13    16    20     3
247    15    13    16    18     3
248    15    13    16    17     3
249    15    13    16    20     3
250    13    15    24    25     3
251   13    15    24    26     3
252    30    31    33    35     3
253    12    10    13    14     3
254    12    10    13    15     3
255    12    10    13    16     3
256    11    10    13    14     3
257    11    10    13    15     3
258    11    10    13    16     3
259    32    31    33    35     3
260    31    33    35    36     3
261    31    33    35    39     3
262    28    27    29    30     3
263    27    29    30    31     3
264    27    29    30    40     3
265    34    33    35    36     3
266    34    33    35    39     3
267     5     6     9    10     3

The output:

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations

ERROR 1 [file p2gout_GDP.itp, line 234]:
  No default Ryckaert-Bell. types


ERROR 2 [file p2gout_GDP.itp, line 236]:
  No default Ryckaert-Bell. types


ERROR 3 [file p2gout_GDP.itp, line 251]:
  No default Ryckaert-Bell. types


ERROR 4 [file p2gout_GDP.itp, line 252]:
  No default Ryckaert-Bell. types


ERROR 5 [file p2gout_GDP.itp, line 259]:
  No default Ryckaert-Bell. types


ERROR 6 [file p2gout_GDP.itp, line 260]:
  No default Ryckaert-Bell. types


ERROR 7 [file p2gout_GDP.itp, line 261]:
  No default Ryckaert-Bell. types


ERROR 8 [file p2gout_GDP.itp, line 265]:
  No default Ryckaert-Bell. types


ERROR 9 [file p2gout_GDP.itp, line 266]:
  No default Ryckaert-Bell. types


ERROR 10 [file p2gout.top, line 28]:
  Invalid directive molecule


-------------------------------------------------------
Program grompp, VERSION 4.6-beta3
Source code file: /home/agent47/gromacs-4.6-beta3/src/kernel/grompp.c,
line: 482

Fatal error:
No molecules were defined in the system
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Thank you
With Regards
Abhishek Acharya


> Dear Gromacs Users.
> I generated a topology file of GDP for OPLSAA force field using MKTOP. But
> on running grompp I got a list of No default Angle types and No default
> Ryckaert Bell. types error. So this time i manually assigned the
> appropriate atom types by looking up the atomtypes.atp file and managed to
> come down from 24 errors to 9 errors. All the errors correspond to missing
> dihedrals only. I notice that these missing dihedrals are concentrated
> around two specific region of the structures which are the Pyramidine ring
> of Guanine and the bond connecting the C1 atom of ribose and N9 atom of
> the imidazole ring of Guanine.
>
> So i have a two part query:
>
> 1. I had assigned the atom types for the Guanine part of GDP from the
> already defined atom types for Guanine in the library. Is it not then
> surprising to get 6 missing dihedrals for the pyramidine ring considering
> the fact that Guanine is already parameterized ? Am i wrong in this ?
>
> 2. In an effort to remove the missing dihedral errors related to the C1-N9
> region it tried to manually add the missing diherals to the ffbonded.itp
> file.
> I noticed one of the missing dihedral was: OH-CT-CT-NA (O2'-C2'-C1'-N9).
>  So i added the dihedral entry as:
> NA     CT     CT     OH      3     16.73600 -16.73600   0.00000   0.00000
>  0.00000   0.00000
>  based on an already defined dihedral:
> NT     CT     CT     OH      3     16.73600 -16.73600   0.00000   0.00000
>  0.00000   0.00000.
> But the error corresponding to this dihedral remained on re-run.
> Is there anything wrong with this ? Do i need to edit some other related
> files.
>
> I am very new to gromacs. Kindly help as I'm stuck.
> Thanks in advance.
> Abhishek Acharya
> M.Tech
> Structural Biology Lab
> Biological Sciences and Bioengineering Department
> Indian Institute of Technology Kanpur.
> --
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