Hello Jinpeng,
Thanks very much for your interest in our work!
I guess that you have build the parameter files for the Cu2+ dummy model
(lib, frcmod),
but there are no dummy atoms but only one Cu atom in your pdb file, as
you showed.
You should also include the dummy atoms in the pdb file, then load it
with tleap.
By the way, we developed the model with OPLS-AA force filed and TIP4P
water model,
Due to the differences between OPLS-AA and AMBER force fields, you have
to validate
the converted parameters in Amber.
All the best,
Qinghua
On 02/23/2017 12:59 PM, JinpengYang wrote:
> Dear professor:
> When I used cationic dummy model to simulate Cu2+ binding ligand,the pdb file is as below:
> HETATM 1 Cu CUB 1 0.449 -0.019 0.904 1.00 0.00 Cu
> HETATM 2 Cl Cl- 8 0.208 0.588 3.088 1.00 0.00 Cl
> HETATM 3 Cl Cl- 9 0.705 -2.258 1.285 1.00 0.00 Cl
> HETATM 4 O1 MPA 10 2.821 0.495 0.268 1.00 0.00 O
> HETATM 5 O2 MPA 10 4.285 -0.851 -0.839 1.00 0.00 O
> HETATM 6 N1 MPA 10 -0.274 1.805 0.149 1.00 0.00 N
> HETATM 7 N2 MPA 10 0.709 -0.353 -1.280 1.00 0.00 N
> HETATM 8 C5 MPA 10 -8.216 -0.474 1.281 1.00 0.00 C
> ...
> And the Cu2+ dummy model is that Cu2+ is surrounded by 6 dummy atoms(from D1 to D6) as Liao did (Liao, Q.; Kamerlin, S. C. L.; Strodel, B. Development and Application of a Non-Bonded Cu2+ Model That Includes the Jahn-Teller Effect. J. Phys. Chem. Lett. 2015, 6, 2657−2662.) Howerer,when using XLeap to loadpdb the pdb file as shown above. The problem arose as belew:
>
> ERROR: Comparing atoms
> .R< 1>.A<D4 5>,
> .R< 1>.A<D3 4>,
> .R< 1>.A<D2 3>, and
> .R< 1>.A<D1 2>
> to atoms
> .R< 1>.A<D4 5>,
> .R< 1>.A<D3 4>,
> .R< 1>.A<D5 6>, and
> .R< 1>.A<D1 2>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named D5 from did not match !
> !
> !ABORTING.
>
>
> The Atom D5 is dummy atom for cationic dummy model.Why did the problem arise ? And what should I do ? Your any advice will help me a lot!
>
> All the regard,
> JinpengYang
>
>
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Received on Thu Feb 23 2017 - 04:30:03 PST
