On Sat, Jan 08, 2011, Sangita Kachhap wrote:
> As you said I generate the new template for phosphoaspartate in mol2 format
> using antechamber as well as library for it, then I use this template and
> library to change ASP 54 to phosphoaspartate in my PDB file.
>
> This worked and now PDB file have phosphoaspartate but this residue is
> conneted at its both ends via TER card.
Here is what is in your "c3wDosR.1-PHD_tleap.pdb" file:
ATOM 789 C LEU 53 44.689 35.370 29.214 1.00 0.00 C
ATOM 790 O LEU 53 44.042 34.326 29.141 1.00 0.00 O
TER
ATOM 791 N PHD 54 45.714 35.565 30.057 1.00 0.00 N
ATOM 792 CA PHD 54 46.161 34.673 31.077 1.00 0.00 C
ATOM 793 C PHD 54 45.912 35.416 32.356 1.00 0.00 C
ATOM 794 O PHD 54 46.188 36.613 32.452 1.00 0.00 O
ATOM 795 CB PHD 54 47.672 34.413 30.979 1.00 0.00 C
ATOM 796 CG PHD 54 48.112 33.530 32.134 1.00 0.00 C
ATOM 797 OD1 PHD 54 47.242 32.857 32.746 1.00 0.00 O
ATOM 798 OD2 PHD 54 49.337 33.532 32.428 1.00 0.00 O
ATOM 799 P PHD 54 47.252 32.201 34.244 1.00 0.00 P
ATOM 800 OP1 PHD 54 46.111 31.224 34.242 1.00 0.00 O
ATOM 801 OP2 PHD 54 48.497 31.492 34.508 1.00 0.00 O
ATOM 802 OP3 PHD 54 47.092 33.374 35.187 1.00 0.00 O
ATOM 803 HB3 PHD 54 47.919 33.917 30.029 1.00 0.00 H
ATOM 804 HB2 PHD 54 48.238 35.355 31.006 1.00 0.00 H
ATOM 805 HA PHD 54 45.654 33.697 31.058 1.00 0.00 H
ATOM 806 H2 PHD 54 45.339 36.459 30.303 1.00 0.00 H
ATOM 807 H PHD 54 45.775 35.295 29.097 1.00 0.00 H
TER
ATOM 808 N VAL 55 45.375 34.720 33.374 1.00 0.00 N
ATOM 809 H VAL 55 46.351 34.677 33.116 1.00 0.00 H
The "TER" cards above tell tleap to make the PHD residue a separate chain,
with no covalent bonds to residues 53 and 55. This is not what you want.
Edit the PDB file and remove those cards, then load the edited file back into
tleap.
...dac
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Received on Sat Jan 08 2011 - 05:30:04 PST
