On 3/24/20 3:26 PM, Daniel Bauer wrote:
Hi, I am trying to convert forcefield parameters of zwitterionic glycine from an amber object file format to gromacs .rtp (to use it with amber99sb, which lacks zwitterionic amino acids). The amber library file I plan to use can be found here: https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/zaa.off This is what i have so far: [ZG] [ atoms ] N N3 -0.408600 1 H1 H 0.300300 2 H2 H 0.300300 3 H3 H 0.300300 4 CA CT -0.026400 5 HA1 H1 0.073800 6 HA2 H1 0.073800 7 C C 0.835500 8 O O2 -0.724500 9 OXT O2 -0.724500 10 [ bonds ] N H1 N H2 N H3 N CA CA HA1 CA HA2 CA C C O C OXT However, I am unsure about the correct conversion of impropers. In the .off file format, those are based on the atom type, while gromacs expects them to be based on atom names. This leaves room for some ambiguity when the same atom type is used multiple types (i.e the COO or NH3 group). The improper parameter section of the .off file looks like this: !entry.zaa_improper.parm.torsions table str type1 str type2 str type3 str type4 int type dbl kp int n dbl p0 str desc "CT" "O2" "C" "O2" 1 10.500000 2 3.141594 "" "CT" "N" "C" "O" 1 10.500000 2 3.141594 "" Now, for the CT-O2-C-O2 improper, this would map to two possible combinations: [ impropers ] ; atom1 atom2 atom3 atom4 phase(deg) kd(kJ/mol-1rad-2) dn CA O C OXT 180 43.932 2 CA OXT C O 180 43.932 2 Are both entries required in the gromacs [ improper ] section or must I put only one of them?
You only need one, otherwise you end up with double the intended strength of the improper.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
