Hi Maggin, Why do you run EM with constraints?
Cheers, Tsjerk On Thu, Jun 13, 2013 at 10:53 AM, maggin <maggin.c...@gmail.com> wrote: > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
