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
