[gmx-users] Re: distance_restraints

[Tsjerk Wassenaar]

Hi Maggin,

Why do you run EM with constraints?

Cheers,

Tsjerk


On Thu, Jun 13, 2013 at 10:53 AM, maggin <maggin.chen at 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
>
>
>
>
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.