Quoting SeungPyo Hong <[EMAIL PROTECTED]>: > Dear gmx-users, > > I want to perform MD with or withou phosphorylated proteins and to compare > their differences. > Because the phosphorylation is well known phenomena, I guess there some of > you had done MD with it. > I will be glad if you let me know where can I found reliable parametered, or > residue topologies, for the phosphorylated amino acid.
The Gromos96 43a1p parameter set includes entries for phosphotyrosine, phosphoserine, and phosphothreonine. The contributed files on the Gromacs website are formatted for an older version of Gromacs, and I have re-formatted them for use with newer versions. Contact me off-list if you want the files; I'm happy to send them to you. If you want phosphohistidine parameters, search the list archive for the relevant discussion. -Justin > > Sincerely > Seungpyo Hong. > -- > -------------------------------------------------- > 'God used beautiful mathematics in creating the world.' > -Paul Dirac > 'But he created too many objects.' > -Seungpyo Hong > > Seungpyo Hong > Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea > Tel. (82)-18-372-2468 > [EMAIL PROTECTED] > [EMAIL PROTECTED] > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
