Tanks for reply.
I edited the PDB file remove TER card. When load it to tleap
with frcmod file and lib file tleap again adding TER card to thses position
> 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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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sat Jan 08 2011 - 07:30:02 PST
