[gmx-users] Re: distance_restraints

[maggin]

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


                             



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