friendli wrote: > Dear all, > > When I performing mutation free energy calculation from Leu to Ala, I > first turn off the charge on the side chain of Leu. As I read from the > GMX archive, the dG/dl curve should be rather smooth for turning off the > partial charge. > In this step(charge off/on), however, I can not obtain the expected > smooth dGdl curve.(see the attachment). I did not use soft-core in this > step. > Is this normal because the mutation is relatively large? If not, what > could be the problem?
The partial charges of the sidechaines of apolar AA (such as Leu) are almost zero, that's why your dGdl is almost zero. Only because of the small dgdl your curve looks non-smooth, but that's just a scale issue here. Best, Jochen > > > the following is part of the topology file. > > 17 opls_238 2 LEU N 7 -0.5 14.0067 ; > qtot 0.5 > 18 opls_241 2 LEU H 7 0.3 1.008 ; > qtot 0.8 > 19 opls_224B 2 LEU CA 7 0.14 12.011 ; > qtot 0.94 > 20 opls_140 2 LEU HA 7 0.06 1.008 ; > qtot 1 > 21 opls_136 2 LEU CB 8 -0.12 12.011 > opls_136 0 12.011 ; qtot 0.88 > 22 opls_140 2 LEU HB1 8 0.06 1.008 > opls_140 0 1.008 ; qtot 0.94 > 23 opls_140 2 LEU HB2 8 0.06 1.008 > opls_140 0 1.008 ; qtot 1 > 24 opls_137 2 LEU CG 9 -0.06 12.011 > opls_137 0 12.011 ; qtot 0.94 > 25 opls_140 2 LEU HG 9 0.06 1.008 > opls_140 0 1.008 ; qtot 1 > 26 opls_135 2 LEU CD1 10 -0.18 12.011 > opls_135 0 12.011 ; qtot 0.82 > 27 opls_140 2 LEU HD11 10 0.06 1.008 > opls_140 0 1.008 ; qtot 0.88 > 28 opls_140 2 LEU HD12 10 0.06 1.008 > opls_140 0 1.008 ; qtot 0.94 > 29 opls_140 2 LEU HD13 10 0.06 1.008 > opls_140 0 1.008 ; qtot 1 > 30 opls_135 2 LEU CD2 11 -0.18 12.011 > opls_135 0 12.011 ; qtot 0.82 > 31 opls_140 2 LEU HD21 11 0.06 1.008 > opls_140 0 1.008 ; qtot 0.88 > 32 opls_140 2 LEU HD22 11 0.06 1.008 > opls_140 0 1.008 ; qtot 0.94 > 33 opls_140 2 LEU HD23 11 0.06 1.008 > opls_140 0 1.008 ; qtot 1 > 34 opls_235 2 LEU C 12 0.5 12.011 ; > qtot 1.5 > 35 opls_236 2 LEU O 12 -0.5 15.9994 ; > qtot 1 > > thank you > > Qiang > > > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
