[gmx-users] question

[Satyan Sharma]

shahrbanoo karbalaee wrote:
>
> Dear
>
> I donot get your answer.I have a peptide with NH2 bond in C terminal.Can
> I run MD with gromacs generally ?.or It  shall know   that as modified
> residue.
> when I run it  I have this error: I donot find c for 14 residue.(it is
> NH2 in c terminal).

Though it would not harm if you read chapter5 of manual before diving into
simulaitons. Mark is right, in the sense that people have to take time out
to answer you queries, when you dont have time to ask quetion with
details.
To help you out, heres what I would do.
Lest say you have glycine in C terminus:
ATOM  10779  N   GLY D3290      78.590 153.920  -4.727  1.00 39.48
ATOM  10780  CA  GLY D3290      77.333 154.511  -4.322  1.00 39.26
ATOM  10781  C   GLY D3290      76.169 153.551  -4.502  1.00 39.05
ATOM  10782  O   GLY D3290      75.018 153.908  -4.242  1.00 39.50
END

Add the N of NH2 and your modified file will be now:
ATOM  10779  N   GLY D3290      78.590 153.920  -4.727  1.00 39.48
ATOM  10780  CA  GLY D3290      77.333 154.511  -4.322  1.00 39.26
ATOM  10781  C   GLY D3290      76.169 153.551  -4.502  1.00 39.05
ATOM  10782  O   GLY D3290      75.018 153.908  -4.242  1.00 39.50
ATOM  10783  N   NH2 D3291      76.460 152.331  -4.946  1.00 38.03
 where Atom 10783 would be NH2 terminus. You can add this NH2 using any
graphics program .. or you can even modify one of the O in COO- terminus.

Now run pdb2gmx with -ter option and select option 2 for Cterminus like
below

Opening library file
/share/apps/gromacs-3.3.1/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Select N-terminus type (start)
 0: GLY-NH3+
 1: NH2
 2: None
1
N-terminus: NH2
Select C-terminus type (end)
 0: COO-
 1: COOH
 2: None
2
C-terminus: None
Now there are 2 residues with 9 atoms
Making bonds...

Thats all...Hope it helps

-Satyan


 >"NH2 bond in C terminal" doesn't yet make any
sense.

>Mark