Justin, Am I correct that X2TOP uses only N2T file to make a topology?
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. 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
