Dear Justin, I was trying to model a part of the protein involved in the active site and these terminal residues i think have no role in active site as per the literature, so i was removing the residues whose coordinates were not properly assigned (missing H atoms) so the initial terminus changed to serine, we can even find such problems in crystal structures where the coordinates don't get resolved properly...I think as the number of residues changed the total charge also changed, these are some of the limitations that i think occur to exactly predict the structure and activity for some proteins.
Thanks Ram On Tue, Sep 29, 2009 at 10:16 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks and as per suggestion, now i have corrected the original >> modelled pdb file and executed the pdb2gmx command with n-terminus >> option 1 (NH2) and C-terminus option 1 (COOH), now the net charge is >> 11.00, and the toplogy file has the first and last residues as under: >> >> >> 1 NL 1 SER N 1 -0.66 14.0067 >> ; qtot -0.66 >> 2 H 1 SER H1 1 0.44 1.008 >> ; qtot -0.22 >> 3 H 1 SER H2 1 0.44 1.008 >> ; qtot 0.22 >> 4 CH1 1 SER CA 1 -0.22 13.019 ; >> qtot 0 >> 5 CH2 1 SER CB 2 0.266 14.027 >> ; qtot 0.266 >> 6 OA 1 SER OG 2 -0.674 15.9994 >> ; qtot -0.408 >> 7 H 1 SER HG 2 0.408 1.008 ; >> qtot 0 >> 8 C 1 SER C 3 0.45 12.011 >> ; qtot 0.45 >> 9 O 1 SER O 3 -0.45 15.9994 ; >> qtot 0 >> >> 2950 N 285 PRO N 1280 0 14.0067 ; >> qtot 11 >> 2951 CH1 285 PRO CA 1281 0 13.019 ; >> qtot 11 >> 2952 CH2R 285 PRO CB 1281 0 14.027 ; >> qtot 11 >> 2953 CH2R 285 PRO CG 1282 0 14.027 ; >> qtot 11 >> 2954 CH2R 285 PRO CD 1282 0 14.027 ; >> qtot 11 >> 2955 C 285 PRO C 1283 0.33 12.011 >> ; qtot 11.33 >> 2956 O 285 PRO OT 1283 -0.45 15.9994 >> ; qtot 10.88 >> 2957 OA 285 PRO O 1283 -0.288 15.9994 >> ; qtot 10.59 >> 2958 H 285 PRO HO 1283 0.408 1.008 ; >> qtot 11 >> >> Please suggest if it is ok, so that i can continue with the further steps. >> > > No, that's your job as a scientist :) Besides, I can't necessarily say. Do > those protonation states model reality? Is your model a reasonable > representation of a true physical system? Does the net charge make sense? > Your original first residue was threonine, now it's serine. What exactly > was your "fix" to this problem? > > These are the things that you should always consider. Only once you've > solved these issues can you proceed with any degree of confidence. > > -Justin > >> >> Thanks, >> >> Ram > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 > _______________________________________________ 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
