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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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