>
> Dear all,
>
> I am currently doing energy minimization of tripeptides in water
> (zwitterionic) with amber 11.
> We came up with the idea to calculate protonated tripeptides, with an
> additional H at the terminal carboxyl group.
> I have calculated the zwitterionic peptides using the ff99SB
> forcefield, but now i have problems loading the *.pdb data with the
> protonated peptide into leap. When i just add the hydrogen atom at the
> end it gets cut off by leap and the normal zwitterion remains, I tried
> renaming it to HXT (like the terminal OXT), but this gives me the
> error that the file contains 1 atom that is not in residue template ALA.
>
> My pdb looks like this
>
> .....
> ATOM 33 N ALA A 3 -0.174 -1.947 -0.288 1.00 0.00
> N
> ATOM 34 H ALA A 3 -0.110 -2.170 -1.293 1.00 0.00
> H
> ATOM 35 CA ALA A 3 0.916 -2.397 0.573 1.00 0.00
> C
> ATOM 36 HA ALA A 3 0.749 -2.093 1.629 1.00 0.00
> H
> ATOM 37 CB ALA A 3 1.011 -3.923 0.523 1.00 0.00
> C
> ATOM 38 HB1 ALA A 3 1.207 -4.268 -0.515 1.00 0.00
> H
> ATOM 39 HB2 ALA A 3 0.061 -4.373 0.879 1.00 0.00
> H
> ATOM 40 HB3 ALA A 3 1.834 -4.280 1.179 1.00 0.00
> H
> ATOM 41 C ALA A 3 2.223 -1.782 0.121 1.00 0.00
> C
> ATOM 42 O ALA A 3 3.363 -2.065 0.788 1.00 0.00
> O
> ATOM 43 OXT ALA A 3 2.256 -1.024 -0.839 1.00 0.00
> O
> ATOM 44 HXT ALA A 3 3.821 -1.308 -0.097 1.00 0.00
> H
> TER
> END
>
> Is there any way i can work around that, i also tried replacing ALA
> with LIG but then i got en error regarding the charge of the unit.
> Is it possible at all to load a charged PDB data?
>
> Thank you in advance
>
> Peter,
> Thorsten
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Received on Thu May 31 2012 - 02:00:03 PDT
