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