Yes, I provided all the possible entries in the N2T.although the problem is the same. I also recreated PDB and re-measured the distances but everything seems pretty correct in my PDB.
N N 2 S 0.17 S 0.17 F F 1 C 0.14 S S 4 O 0.17 O 0.17 C 0.18 N 0.17 C C 4 F 0.14 F 0.14 F 0.14 S 0.18 O O 1 S 0.17 Vitaly On Fri, Feb 5, 2010 at 10:13 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Vitaly V. Chaban wrote: >> >> On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> Vitaly V. Chaban wrote: >>>> >>>> In this context, it is interesting how X2TOP decides that two atoms >>>> are connected? Only on the base of N2T: if the atom should have 4 >>>> neighbours, it looks for the appropriate number of them? >>>> >>> That's correct. >> >> >> Then the interesting error is: >> "Fatal error: >> No forcefield type for atom C (1) with 0 bonds" >> >> while PDB contains other atoms than carbon. If it looks for neighbours >> why does not it find them... >> > > The error is complaining that atom 1 (a carbon atom) is not within searching > distance of any atoms to which it should be bonded. Have you specified .n2t > entries for every one of your atoms? For example, it is insufficient to > specify an .n2t line for the central S (in your original post) and expect > x2top to understand that the O, N, and C atoms to which it is connected can > have their atom types determined. You need .n2t entries for all of those > atoms, too, specifying that they are, in turn, connected to S in some way. > The above error suggests that x2top is finding a carbon atom that you have > not defined in the .n2t file. > > -Justin > >> >> >> >>>> In my case, maybe it considers that 0.18 nm is too much for two atoms >>>> to be connected? >>>> >>> The length defined in the .n2t file should be the actual bond length >>> (from >>> the coordinate file) +/- 10%, like specbond.dat, if I recall; x2top >>> should >>> not arbitrarily try to dictate that a bond is too long. >>> >>> -Justin >>> >>>> ---------- Forwarded message ---------- >>>> From: Vitaly V. Chaban <vvcha...@gmail.com> >>>> Date: Fri, Feb 5, 2010 at 7:56 PM >>>> Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for >>>> atom S (2) with 3 bonds >>>> To: jalem...@vt.edu, gmx-users@gromacs.org >>>> >>>> >>>> Yes. This worked even with my N2T. I will probably recreate my PDB... >>>> >>>> >>>> On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul <jalem...@vt.edu> >>>> wrote: >>>>> >>>>> Vitaly V. Chaban wrote: >>>>>> >>>>>> Justin, >>>>>> >>>>>> Am I correct that X2TOP uses only N2T file to make a topology? >>>>>> >>>>> Yes. >>>>> >>>>>> I made the full line for Sulphur but it didn't change the situation. >>>>>> It looks strange that X2TOP notices 3 bonds although I propose to have >>>>>> 4 bonds (and they are present). If I propose 3 bonds, it readily gives >>>>>> an output... This is like it has predefined Sulphur with 3 bonds. >>>>>> >>>>> Certainly not. Take, for example, a simple SO4 molecule: >>>>> >>>>> REMARK >>>>> HETATM 1 OAC DRG 1 5.850 14.800 -12.770 1.00 20.00 >>>>> O >>>>> HETATM 2 SAE DRG 1 4.810 15.780 -12.710 1.00 20.00 >>>>> S >>>>> HETATM 3 OAD DRG 1 3.550 15.150 -12.980 1.00 20.00 >>>>> O >>>>> HETATM 4 OAB DRG 1 4.770 16.390 -11.340 1.00 20.00 >>>>> O >>>>> HETATM 5 OAA DRG 1 5.070 16.850 -13.730 1.00 20.00 >>>>> O >>>>> >>>>> The topology is generated just fine with this .n2t file: >>>>> >>>>> S S 0 32.06 4 O 0.145 O 0.145 O 0.145 O 0.145 >>>>> O OM 0 15.9994 1 S 0.145 >>>>> >>>>> I don't know what might be going on with your system, but I would >>>>> suggest >>>>> creating an .n2t file with only entries pertinent to your system, for >>>>> all >>>>> atoms involved. This is, of course, only really useful for debugging, >>>>> since >>>>> in theory, x2top should be easily extensible by appending the .n2t >>>>> file. >>>>> >>>>> -Justin >>>>> >>>>>> Vitaly >>>>>> >>>>>> >>>>>> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban <vvcha...@gmail.com> >>>>>> wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> This can be the reason when X2TOP gives the following error: >>>>>>> " >>>>>>> Fatal error: >>>>>>> No forcefield type for atom S (2) with 3 bonds >>>>>>> " >>>>>>> ? >>>>>>> >>>>>>> I try to translate PDB of the TFSA anion >>>>>>> O O >>>>>>> || || >>>>>>> F3C-S-N-S-CF3 >>>>>>> || || >>>>>>> O O >>>>>>> >>>>>>> into topology. >>>>>>> >>>>>>> >>>>>>> My PDB contains optimized geometry: >>>>>>> HEADER TFSA >>>>>>> COMPND TFSA >>>>>>> AUTHOR VVC >>>>>>> ATOM 1 N TFS 1 -0.000 0.444 -0.008 1.00 0.00 >>>>>>> ATOM 2 S TFS 1 1.401 -0.440 -0.189 1.00 0.00 >>>>>>> ATOM 3 S TFS 1 -1.400 -0.438 0.189 1.00 0.00 >>>>>>> ATOM 4 O TFS 1 -1.236 -1.810 -0.833 1.00 0.00 >>>>>>> ATOM 5 O TFS 1 -1.284 -1.009 1.805 1.00 0.00 >>>>>>> ATOM 6 O TFS 1 1.293 -1.026 -1.800 1.00 0.00 >>>>>>> ATOM 7 O TFS 1 1.233 -1.803 0.845 1.00 0.00 >>>>>>> ATOM 8 C TFS 1 -2.837 0.628 -0.107 1.00 0.00 >>>>>>> ATOM 9 C TFS 1 2.836 0.630 0.105 1.00 0.00 >>>>>>> ATOM 10 F TFS 1 -3.996 -0.097 0.093 1.00 0.00 >>>>>>> ATOM 11 F TFS 1 -2.805 1.094 -1.408 1.00 0.00 >>>>>>> ATOM 12 F TFS 1 -2.807 1.698 0.766 1.00 0.00 >>>>>>> ATOM 13 F TFS 1 2.802 1.099 1.404 1.00 0.00 >>>>>>> ATOM 14 F TFS 1 2.803 1.698 -0.771 1.00 0.00 >>>>>>> ATOM 15 F TFS 1 3.996 -0.093 -0.093 1.00 0.00 >>>>>>> END >>>>>>> >>>>>>> and my n2t file is >>>>>>> >>>>>>> C C 1 C ; CNT Carbon with one bond >>>>>>> C C 2 C C : CNT double bonded Carbon >>>>>>> O O 1 C ; CARBONYL OXYGEN (C=O) >>>>>>> O OM 1 C ; CARBOXYL OXYGEN (CO-) >>>>>>> O OA 2 C H ; HYDROXYL OXYGEN (OH) >>>>>>> O OW 2 H H ; WATER OXYGEN >>>>>>> N N 3 H C C ; PEPTIDE NITROGEN (N OR NH) >>>>>>> N NT 3 H H C ; TERMINAL NITROGEN (NH2) >>>>>>> N NL 4 C H H H ; TERMINAL NITROGEN (NH3) >>>>>>> N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS) >>>>>>> N NR5* 3 C C H ; AROMATIC N (5-RING,3 BONDS) >>>>>>> N NP 3 C C FE ; PORPHYRIN NITROGEN >>>>>>> C C 3 C O * ; BARE CARBON (PEPTIDE,C=O,C-N) >>>>>>> ; Note that order is importante here because of wildcards. >>>>>>> C C3 4 H H H * ; ALIPHATIC CH3 GROUP >>>>>>> C C2 4 H H C * ; ALIPHATIC CH2 GROUP >>>>>>> C C1 4 H C * * ; ALIPHATIC CH GROUP >>>>>>> C CB 3 C C C ; BARE CARBON (5-,6-RING) >>>>>>> H H 1 N ; HYDROGEN BONDED TO NITROGEN >>>>>>> H HO 1 O ; HYDROXYL HYDROGEN >>>>>>> H HW 1 OW ; WATER HYDROGEN >>>>>>> H HS 1 S ; HYDROGEN BONDED TO SULFUR >>>>>>> H HC 1 C ; HYDROGEN BONDED TO CARBON >>>>>>> S S 4 C 0.181 N 0.167 O 0.172 O 0.172 >>>>>>> F F 1 C >>>>>>> >>>>>>> >>>>>>> >>>>>>> The Sulphur atoms have each 4 bonds but X2TOP wants them to have only >>>>>>> 3. If I change the string in the N2T to 3 bonds, the topology is >>>>>>> generated but S-C bond is absent. >>>>>>> >>>>>>> What can be the problem? >>>>>>> >>>>>>> Thanks. >>>>>>> -- >>>>>>> Vitaly V. Chaban, Ph.D. >>>>>>> http://www-rmn.univer.kharkov.ua/chaban.html >>>>>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html -- 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/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/mailing_lists/users.php
