Hi, Justin, It's seems no problem at steep energy minimization, except lose H atoms connect with C, the superposition are very well.
When I use Pymol to align the NMR structure and the structure after cg minimization, because cg is after steep, so same as steep, they lose H atoms that connect with C. but superposition is not so good with steep. It seems have some distanc and angles between problematic areas, and also as to good areas. problematic areas: atom1 atom2 1 N1+ (GLY124 N) 4 H (GLY124 HT3) <http://gromacs.5086.x6.nabble.com/file/n5009127/GLY124_cg.png> atom1 atom2 181 C (PRO137 CD) 182 H (PRO137 HD1) <http://gromacs.5086.x6.nabble.com/file/n5009127/PRO137_cg.png> atom1 atom2 262 H (PHE141 HD1) 263 C (PHE141 CE2) <http://gromacs.5086.x6.nabble.com/file/n5009127/PHE141_cg.png> atom1 atom2 296 O1- (ASP144 OD2) 297 C (ASP144 C) <http://gromacs.5086.x6.nabble.com/file/n5009127/ASP144_cg.png> atom1 atom2 685 O (PRO165 O) <http://gromacs.5086.x6.nabble.com/file/n5009127/PRO165_cg.png> atom1 atom2 685 O (PRO165 O) 688 C (VAL166 CA) <http://gromacs.5086.x6.nabble.com/file/n5009127/VAL166_cg.png> good area: PRO158 <http://gromacs.5086.x6.nabble.com/file/n5009127/PRO158_cg.png> analysis: 1) 1 N1+ (GLY124 N) 4 H (GLY124 HT3) because GLY124 is N-end, and have a positive charge, so after cg minimization, it move long range, so have LINCS WARNING 2)181 C (PRO137 CD) 182 H (PRO137 HD1) because at steep minimization, it lose HD1, so at cg minimization, it also lost HD1, so actually they have no bond, 3) 262 H (PHE141 HD1) 263 C (PHE141 CE2) 296 O1- (ASP144 OD2) 297 C (ASP144 C) 685 O (PRO165 O) 688 C (VAL166 CA) It seems for this group, atoms are far away, they are not form bond, but it looks cg take they as bonds, so it cause LINCS WARNING At such situation, what is the best way to deal with these LINCS WARNINGS? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009127.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
