Hi! You are completely right about the parametrization. I found the pyrodoxal in charmm and I think I am going to start over to combine it with lys which can reduce input from outside source to make charmm happy. however I left the md.mdp run yesterday and this morning i found the methyl group is fixed, the ring went back to flat... not quite sure what happened between minimization and simulation. but yes I wouldn't really trust the results based on the discrepancies. Thanks for the advice :)
Ming On Tue, Jan 16, 2018 at 7:37 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/16/18 6:38 AM, MD wrote: > >> Hi Justin, >> >> I got the itp and parameters of my side chain modified amino acid from >> CHARMM-GUI and incorporated it into my protein structure, labeled with >> HETATM. I made the atom types names consistent with charmm forcefield >> which >> I used with gromacs and made sure overall the parameters look decent for >> now. After some fixing the grompp would run with no warnings, and I did a >> quick energy minimization, but ended up with a distorted six member ring. >> I >> have the picture and my parameters attached. Your time is appreciated :) >> >> https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI- >> rgIesxy0QdIHm7tqTug/edit?usp=sharing >> > > You have a number of problems. If that's simply pyridoxal phosphate linked > with lysine, then you have lots of missing H atoms and the protonation > state of your phosphate group is incorrect, at least with respect to normal > physiological pH. You're getting a lot of distortion from a lot of places, > not the least of which is that you should have a methyl group attached to > the ring, not a methylene (=CH2), as that changes the conjugation entirely. > > Also, as I said before - *do not* mix CGenFF and standard CHARMM > parameters. You can't just change around atom types until grompp warnings > go away. What you're seeking to do is complicated and requires great care, > otherwise you get garbage. There's no magic push-button here. You've got to > do a thorough parametrization, including all the things I said before. > Anything short of that, in this instance, is likely to fail. You can take > initial guess charges from existing groups in CHARMM, without even going to > CGenFF, as most of those groups should already be well described. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.