[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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