[gmx-users] Removing errors related to missing dihedrals.
Abhishek Acharya
aacharya at iitk.ac.in
Thu Feb 14 17:54:41 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 ?
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.
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
More information about the gromacs.org_gmx-users
mailing list