[gmx-users] Re: distance_restraints
jalemkul at vt.edu
Wed Jun 12 11:40:43 CEST 2013
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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