Dear Justin, Thanks for the suggestions and will be back after sometime after following the trials.
Ram On Tue, Sep 29, 2009 at 10:45 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> 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 > > Crystal structures never have H, but we simulate them all the time. Their > geometry is largely predictable :) > > Consider whether or not these deletions will have an effect. While not > catalytically active, do they have any role in maintaining the protein's > structure? Just my $0.02. Don't chop out what doesn't seem to work; it > might (or might not) be important. > > -Justin > >> 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 >>> >> > > -- > ======================================== > > 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
