[gmx-users] Removing errors related to missing dihedrals.
Justin Lemkul
jalemkul at vt.edu
Tue Feb 12 14:07:27 CET 2013
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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