[gmx-users] Cl topology in gromacs

[Mark Abraham]

Sounds like a question for the acpype developers directly :-)

Mark

On Wed, Aug 19, 2015 at 8:52 AM Albert <mailmd2011 at gmail.com> wrote:

> 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
> --
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