[gmx-users] endcapping

[w.j.schravendijk at students.pharm.uu.nl]

It seemed that the input from the original pdb file:

ATOM    200  NE2 GLN A  26      14.304  -0.117  15.290  1.00 57.61
HETATM  201  N   NH2 A  27      13.279   5.297  18.956  1.00 48.71
TER     202      NH2 A  27

Was not completely recognized. After a short struggle, I edited a gromacs
pdb output to :

ATOM    262  O   GLN A  26      11.409   5.344  17.597  1.00  0.000
ATOM    259  N   NH2 A  26      13.131   5.276  18.670  1.00  0.000
ATOM    260  H1  NH2 A  26      14.069   4.941  18.576  1.00  0.000
ATOM    261  H2  NH2 A  26      12.536   5.748  19.321  1.00  0.000

Which passed pdb2gmx -ter (with no endgroups) and grompp with no errors.
Still, this amide is not completely planar (while the amide in GLN is),
but that is not a real issue here.

Thanx for helping!

Greetings, Pim

On Tue, 19 Feb 2002, David van der Spoel wrote:

> It is not at all necessary to change any files for an NH2 endgroup if you
> have an N atom present (like you have) as long as it has a different
> residue number than the previous residue. You do
> pdb2gmx -ter
> and select none for the c-terminus
> that's all
>
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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