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.
