[gmx-users] Removing errors related to missing dihedrals.
Abhishek Acharya
aacharya at iitk.ac.in
Thu Feb 14 22:15:44 CET 2013
> Hello Justin
> Thank you very much for your effort and help. I will try adding new
> parameter corresponding to the errors. Meanwhile just out of curiosity and
> possible need, what should be done in case no matching parameters are
> found for the missing dihedrals? I see that there are 6 fields in the
> dihedrals section of ffbonded.itp. How do we calculate these parameters
> for new dihedrals ?
I wanted to go step by step. I first tried to address the errors 1, 2 and
3. So I added the following dihedrals to ffbonded.itp.
For Error1:
HC CT CT NA 3 -4.09614 5.08775 2.96645 -3.95806
0.00000 0.00000
from:
HC CT CT NT 3 -4.09614 5.08775 2.96645 -3.95806
0.00000 0.00000 ; amine all-atom
For Error2
OH CT CT NA 3 9.89307 -4.71746 3.67774 -8.85335
0.00000 0.00000
from:
N3 CT_2 CT OH 3 9.89307 -4.71746 3.67774 -8.85335
0.00000 0.00000 ; Chi for Ser & Thr
For Error3
CT OS CT NA 3 -5.23000 7.32200 6.27600 -8.36800
0.00000 0.00000
from:
CT OS CT N 3 -5.23000 7.32200 6.27600 -8.36800
0.00000 0.00000 ; (From wildcard) imidazoles, indoles, purines
I expected this to remove the errors 1, 2 and 3. I took care to keep the
atomtypes order the same. But this doesn't seem to affect the result. I
get the same errors. Any ideas??
>
> Thank you again
> With regards
> Abhishek
>>
>> 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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>
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