Hello:
I am using acpype to create ligand topology. However, I noticed that
acpype may not recogonize Cl element which is a halogen atom correctly.
After acpype, it generate a new ligand pdb file called: lig_NEW.pdb and
I found the following:
ATOM 10 C09 UNK Z 1 11.502 -10.939 3.783 1.00
0.00 C
ATOM 11 CL11 UNK Z 1 10.314 -10.335 4.933 1.00
0.00 C
ATOM 12 C12 UNK Z 1 12.865 -10.938 4.098 1.00
0.00 C
ATOM 13 CL13 UNK Z 1 13.389 -10.333 5.666 1.00
0.00 C
atom CL11 and CL13 are halogen atom, but it seems that acpype treat them
as carbon which is wrong.... I am just wondering how can we solve this
problem?
thx a lot
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Received on Wed Aug 19 2015 - 00:30:03 PDT
