[gmx-users] Re: distance_restraints

[Justin Lemkul]

On 6/12/13 12:10 AM, maggin wrote:
> Hi, Justin,
>
> You are right, I should first fix the bad geometry.
>
> I check 1dx0.pdb, and the problematic areas are:
> atom1                                 atom2
>        1  N1+  (GLY124   N)             4 H  (GLY124  HT3)
>     181  C      (PRO137  CD)        182 H  (PRO137  HD1)
>     262  H      (PHE141  HD1)      263 C  (PHE141  CE2)
>     296 O1-    (ASP144  OD2)      297 C  (ASP144  C)
>     685 O       (PRO165  O)          688 C  (VAL166 CA)
>
> for these atoms bonds that rotated more than 30 degrees
>
>
> 1dx0.pdb is get from NMR.
>
> So, for the initial structure , is there anyways to solve these LINCS
> WARNING ?
>

What does visual inspection tell you about these areas: (1) from the NMR 
structure and (2) after steep minimization?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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