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... >> 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 > > ======================================== > -- 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? 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