Hi all Very sorry for my stupid question .. I really work a lot on these problem
I wish to use Trifluroethanol as solvent for my study ... I Check the top file for G96 53a6 ff It shows TFE with following lines ... [ TFE ] [ atoms ] HT H 0.41000 0 OT OTFE -0.62500 0 CH2T CHTFE 0.27300 0 CT CTFE 0.45200 0 F1T FTFE -0.17000 0 F2T FTFE -0.17000 0 F3T FTFE -0.17000 0 [ bonds ] HT OT gb_1 OT CH2T gb_18 CH2T CT gb_27 CT F1T gb_13 CT F2T gb_13 CT F3T gb_13 [ angles ] ; ai aj ak gromos type HT OT CH2T ga_50 OT CH2T CT ga_51 CH2T CT F1T ga_52 CH2T CT F2T ga_52 CH2T CT F3T ga_52 F1T CT F2T ga_49 F1T CT F3T ga_49 F2T CT F3T ga_49 [ impropers ] ; ai aj ak al gromos type [ dihedrals ] ; ai aj ak al gromos type HT OT CH2T CT gd_24 I draw TFE with Avogadro software... I get following pdb .. COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.0 HETATM 1 C LIG 1 -7.301 3.857 0.070 1.00 0.00 C HETATM 2 C LIG 1 -6.798 2.416 0.102 1.00 0.00 C HETATM 3 F LIG 1 -8.626 3.915 0.327 1.00 0.00 F HETATM 4 F LIG 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM 5 F LIG 1 -6.668 4.631 0.977 1.00 0.00 F HETATM 6 O LIG 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM 7 H LIG 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM 8 H LIG 1 -6.898 2.006 1.111 1.00 0.00 H HETATM 9 H LIG 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT 1 2 3 4 5 CONECT 1 CONECT 2 1 6 7 8 CONECT 2 CONECT 3 1 CONECT 4 1 CONECT 5 1 CONECT 6 2 9 CONECT 7 2 CONECT 8 2 CONECT 9 6 MASTER 0 0 0 0 0 0 0 0 9 0 9 0 END I change pdb as follow to match the nomenclature with G96 53a6 ff (Is it right or wrong ????) OMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.0 HETATM 1 CT TFE 1 -7.301 3.857 0.070 1.00 0.00 C HETATM 2 CH2T TFE 1 -6.798 2.416 0.102 1.00 0.00 C HETATM 3 F1T TFE 1 -8.626 3.915 0.327 1.00 0.00 F HETATM 4 F2T TFE 1 -7.094 4.399 -1.153 1.00 0.00 F HETATM 5 F3T TFE 1 -6.668 4.631 0.977 1.00 0.00 F HETATM 6 OT TFE 1 -5.426 2.272 -0.294 1.00 0.00 O HETATM 7 H TFE 1 -7.399 1.800 -0.574 1.00 0.00 H HETATM 8 H TFE 1 -6.898 2.006 1.111 1.00 0.00 H HETATM 9 HT TFE 1 -5.299 2.795 -1.107 1.00 0.00 H CONECT 1 2 3 4 5 AFTER running pdb2gmx -ignh I got following error .... ------------------------------------------------------ Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue 'F' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I tried a lot ... Please give me some suggestion ... Thank you in Advance ... Rama David ...
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