On 2/12/13 6:19 AM, Abhishek Acharya wrote:
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
You haven't listed what you've done to try to address these (i.e., what you
added to ffbonded.itp), so it's still somewhat hard to help. I will list here
the correct order of atomtypes, in the hopes that it helps you match suitable
parameters. Order of atomtypes may matter. I see that you have an issue with a
dihedral of type OH-CT-CT-NA, but you added parameters for NA-CT-CT-OH. In
principle, the order should be matched either way, but you may have to list
atomtypes in the exact same order.
ERROR 1 [file p2gout_GDP.itp, line 234]:
No default Ryckaert-Bell. types
So this one is HC-CT-CT-NA
ERROR 2 [file p2gout_GDP.itp, line 236]:
No default Ryckaert-Bell. types
OH-CT-CT-NA
ERROR 3 [file p2gout_GDP.itp, line 251]:
No default Ryckaert-Bell. types
CT-OS-CT-NA
ERROR 4 [file p2gout_GDP.itp, line 252]:
No default Ryckaert-Bell. types
CB-C-NA-CA
ERROR 5 [file p2gout_GDP.itp, line 259]:
No default Ryckaert-Bell. types
O-C-NA-CA
ERROR 6 [file p2gout_GDP.itp, line 260]:
No default Ryckaert-Bell. types
C-NA-CA-N2
ERROR 7 [file p2gout_GDP.itp, line 261]:
No default Ryckaert-Bell. types
C-NA-CA-NC
ERROR 8 [file p2gout_GDP.itp, line 265]:
No default Ryckaert-Bell. types
H-NA-CA-N2
ERROR 9 [file p2gout_GDP.itp, line 266]:
No default Ryckaert-Bell. types
H-NA-CA-NC
ERROR 10 [file p2gout.top, line 28]:
Invalid directive molecule
Easily fixed by using the right directive name - [molecules], not [molecule].
-Justin
-------------------------------------------------------
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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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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