On 3/9/18 6:55 AM, ABEL Stephane wrote:
Dear all, I am constructing a top file for gramicidin A a short that contains a succession of D- and L-AAs (the exact sequence is HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH) and have a unexpected problem whenI use charmm36 . Indeed it seems that a dihedral parameter is missing in the last charmm36m release for GROMACS but also (?) in the original last CHARMM toppar file (including CHARMM36m). For instance for linking the (D-LEU --> L-TRP) I need the CTD1 C NH1 CT1 (where the CTD1 is the carbon atom type for D-LEU) however I did not find this parameters in the CHARMM36. Am I missing something or did something wrong ?? It is valid to use the values of CTD1 C NH1 CT1.
Yes. The CTD1 atom type is just a clone of CT1, and the parameters for CT1-C-NH1-CTD1 are copied from CT1-C-NH1-CT1, so the parameters for CTD1-C-NH1-CT1 will also be the same as CT1-C-NH1-CT1. I'm not sure why that's never caused a problem before, but I'll get it fixed in both CHARMM and GROMACS.
-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.
