[gmx-users] parameterization of N atom type if ffgmx (continue)

[Daan Virtual]

Hi Alex

Clearly this is not the global energy minimum but a local one - the H
connot flip the other way without moving through a lot of steric
hindrance.

cheers

Daan

On Wed, 16 Oct 2002, alexander yakovenko wrote:

> Hi Daan,
> I am sorry for bad description of my system. There is a pdb of interest fragment of my system (after Gromacs cg em 1000 steps). It locates at hydrophobic pocket and no any addition water or other charged groups near it:
>  --------
> ATOM      1  HI0 LIG B   1      16.830  32.830  30.470
> ATOM      2  O00 LIG B   2      17.150  32.190  31.130
> ATOM      3  CF0 LIG B   3      18.270  32.740  31.660
> ATOM      4  CE0 LIG B   4      18.370  34.130  31.490
> ATOM      5  HF0 LIG B   5      17.572  34.715  31.137
> ATOM      6  CD0 LIG B   6      19.682  34.748  31.746
> ATOM      7  HE0 LIG B   7      19.781  35.794  31.709
> ATOM      8  CB0 LIG B   8      20.757  33.991  32.029
> ATOM      9  CC0 LIG B   9      20.651  32.528  32.098
> ATOM     10  HD0 LIG B  10      21.511  31.953  32.286
> ATOM     11  CG0 LIG B  11      19.463  31.926  31.917
> ATOM     12  HG0 LIG B  12      19.388  30.878  31.957
> ATOM     13  H   LIG B  13      21.710  34.466  32.208
> TER
> ATOM     14  N   HIS A 212      13.850  30.120  31.080
> ATOM     15  H   HIS A 212      14.570  29.540  31.450
> ATOM     16  CA  HIS A 212      13.760  31.500  31.620
> ATOM     17  CB  HIS A 212      14.620  31.690  32.880
> ATOM     18  CG  HIS A 212      14.700  33.140  33.370
> ATOM     19  ND1 HIS A 212      15.530  34.080  32.960
> ATOM     20  CD2 HIS A 212      13.770  33.810  34.050
> ATOM     21  CE1 HIS A 212      15.160  35.300  33.330
> ATOM     22  NE2 HIS A 212      14.050  35.110  34.020
> ATOM     23  HE2 HIS A 212      13.510  35.820  34.470
> ATOM     24  C   HIS A 212      13.980  32.580  30.550
> ATOM     25  O   HIS A 212      13.290  33.590  30.540
> ATOM     26  HA  HIS A 212      12.729  31.639  31.945
> ATOM     27 1HB  HIS A 212      14.237  31.057  33.680
> ATOM     28 2HB  HIS A 212      15.635  31.405  32.603
> ATOM     29  HD2 HIS A 212      12.913  33.362  34.553
> ATOM     30  HE1 HIS A 212      15.659  36.244  33.113
> ATOM     31  N   LEU A 213      14.690  32.210  29.500
> ATOM     32  H   LEU A 213      15.380  31.490  29.580
> ATOM     33  CA  LEU A 213      14.860  33.170  28.400
> ATOM     34  CB  LEU A 213      16.310  33.150  27.840
> ATOM     35  CG  LEU A 213      16.720  34.440  27.080
> ATOM     36  CD1 LEU A 213      16.010  35.700  27.610
> ATOM     37  CD2 LEU A 213      18.220  34.590  27.290
> ATOM     38  C   LEU A 213      13.730  33.190  27.360
> ATOM     39  O   LEU A 213      13.370  34.260  26.860
> ATOM     40  HA  LEU A 213      14.737  34.160  28.838
> ATOM     41 1HB  LEU A 213      17.012  32.970  28.654
> ATOM     42 2HB  LEU A 213      16.340  32.344  27.106
> ATOM     43  HG  LEU A 213      16.053  34.590  26.231
> ATOM     44 1HD1 LEU A 213      16.338  36.569  27.039
> ATOM     45 2HD1 LEU A 213      14.932  35.581  27.504
> ATOM     46 3HD1 LEU A 213      16.258  35.842  28.662
> ATOM     47 1HD2 LEU A 213      18.571  35.485  26.776
> ATOM     48 2HD2 LEU A 213      18.431  34.677  28.356
> ATOM     49 3HD2 LEU A 213      18.732  33.716  26.888
> END
> --------
>
> > Hi Alex
> >
> > It sounds to me like the OH of your ligand is DONATING a hydrogen bond
> > to the ND1 of the histidine and ACCEPTING a hydrogen bond from your
> > backbone nitrogen - there is nothing wrong with that?
> >
> > cheers
> >
> > Daan
> >
> Thank you,
>
> Alexander Yakovenko
> Institute of Molecular Biology & Genetic of NAS of Ukraine
> 03143
> acad.Zabolotnogo str. 150
> Kiev
> Ukraine
> ______________________________________________
> E-mail: yakovenko_a at ukr.net
>
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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