Hi, The sugars were improved in 45a3. The parameters haven't changed for the later versions.
Cheers, Tsjerk On Tue, Apr 13, 2010 at 12:24 AM, Justin A. Lemkul <[email protected]> wrote: > > > Michael McGovern wrote: >> >> Hi everyone. I'm doing some simulations involving the sugar trehalose, >> with the 53a6 force field. There is an odd issue I am having with the rtp >> file for trehalose. It seems to be charged. Here is the beginning of the >> rtp entry: >> >> [ TRH ] >> [ atoms ] >> HO4 H 0.41000 0 >> O4 OA -0.64200 0 >> C4 CH1 0.23200 0 >> C3 CH1 0.23200 1 >> O3 OA -0.64200 1 >> HO3 H 0.41000 1 >> C2 CH1 0.23200 2 >> O2 OA -0.64200 2 >> HO2 H 0.41000 2 >> C6 CH1 0.23200 3 >> O6 OA -0.64200 3 >> HO6 H 0.41000 3 >> C5 CH1 0.37800 4 >> O5 OA -0.45000 4 >> C1 CH1 0.24200 4 >> O1 OA -0.34000 4 >> C1' CH1 0.24200 4 >> O5' OA -0.45000 4 >> C5' CH1 0.37800 4 >> C4' CH1 0.27500 5 >> O4' OA -0.60000 5 >> HO4' H 0.47000 5 >> C3' CH1 0.23200 6 >> O3' OA -0.64200 6 >> HO3' H 0.41000 6 >> C2' CH1 0.23200 7 >> O2' OA -0.64200 7 >> HO2' H 0.41000 7 >> C6' CH1 0.23200 8 >> O6' OA -0.64200 8 >> HO6' H 0.41000 8 >> >> Charge group 5 has a net charge of +0.145. Is this a typo? Should I just >> change it to be the same as the other C-O-H charge groups? >> >> > > The net charge certainly seems wrong. Before making any ad hoc changes, > though, refer to the primary literature for the force field and make sure > everything else is right. I think 53a6 has the same charges as 45a4, > wherein the sugar parameters were improved from 45a3. I don't see any > mention of modifications to sugars in the 53a6 paper. 45a4 ref: > > Lins and Hunenberger (2005) J Comput Chem 26: 1400-1412. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
