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?
In my case, maybe it considers that 0.18 nm is too much for two atoms to be connected? ---------- 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 >>> >> -- 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
