[gmx-users] Cl topology in gromacs

[Albert]

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, it seems that acpype treat them as 
carbon which is wrong.... I am just wondering how can we solve this problem?

thx a lot