On Thu, Mar 24, 2011, thomas.fox.boehringer-ingelheim.com wrote:
>
> here is a simple example, methylene chloride:
>
> The pdb file is:
> HETATM 1 C * 0 0.000 0.000 0.000 1.00 0.00 C
> HETATM 2 CL * 0 1.773 0.000 0.000 1.00 0.00 CL
> HETATM 3 H2 * 0 -0.363 0.727 0.727 1.00 0.00 H
> HETATM 4 H3 * 0 -0.363 -0.993 0.266 1.00 0.00 H
> HETATM 5 H4 * 0 -0.363 0.266 -0.993 1.00 0.00 H
> CONECT 1 3 4 5 2
> CONECT 2 1
> CONECT 3 1
> CONECT 4 1
> CONECT 5 1
> END
>
> The antechamber command:
> antechamber -i test.pdb -fi pdb -o test.prepin -fo prepi
>
> As you can see, the IGRAPH in the prepin file for the chloride has been
> changed from CL -> Cl.
I can confirm that the current developer's code still has this problem. The
problem goes away if the output format is mol2. (Another reason, among many,
to avoid the prepi input if possible.)
I'm cc-ing this to Junmei to see if he has any ideas.
...thanks for the report...dave
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Received on Sat Mar 26 2011 - 18:00:03 PDT
