> 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. >>>> -- >>>> gmx-users mailing list gmx-users@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-requ...@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@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-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists