[gmx-users] Re: Problem with Amber99SB-ILDN ff

[Justin Lemkul]

On 7/9/13 11:23 AM, Melchor S. wrote:
> I am using gromacs 4.5.5, I didn't  tell you yesterday. I have been tried a
> lot of things, but without any success.
>
> One of that I think has to work fine, is with the NGLU nomenclature, but
> when I use it, I obtain this
> There is a dangling bond at at least one of the terminal ends and the force
> field does not provide terminal entries or files. Edit a .n.tdb and/or
> .c.tdb file.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> I am really sure about the structure of the Ligand ( Glu is in a separate
> chain like a ligand) so I don't know what to do.
>
> My PDB file looks like this
>
> .......
> [...]
> ATOM   1896  OXT ALA A 258      -5.158  76.455 109.444  1.00 26.88      A
> TER
> HETATM 1932  N   NGLU B   1      18.161  74.498 104.017  1.00 24.96
> HETATM 1933  CA  NGLU B   1      18.483  73.747 105.315  1.00 22.94
> HETATM 1934  C   NGLU B   1      19.769  73.978 105.618  1.00 27.29
> HETATM 1945  O   NGLU B   1      20.258  74.226 106.781  1.00 28.71
> HETATM 1936  CB  NGLU B   1      18.262  72.255 105.280  1.00 19.40
> HETATM 1937  CG  NGLU B   1      18.556  71.574 106.686  1.00 19.32
> HETATM 1938  CD  NGLU B   1      17.462  71.977 107.666  1.00 21.73
> HETATM 1939  OE1 NGLU B   1      16.330  72.460 107.490  1.00 22.44
> HETATM 1940  OE2 NGLU B   1      17.965  71.816 108.815  1.00 30.0
> HETATM 1941  OXT NGLU B   1      20.862  74.195 104.777  1.00 27.10
> END
>

This is a very different situation, one that pdb2gmx is not equipped to cope 
with.  You don't actually have another protein chain, which your original posts 
seemed to imply.  Instead, you have a zwitterionic form of Glu, which is not 
present in your chosen force field.  You will have to derive its parameters in 
some other manner (other published parameters, acpype, antechamber, etc).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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