Hi Rana,
It is a warning, which may cause problem or may not. You can check with the $AMBERHOME/dat/leap/parm/gaff.dat file about the atom type explanations to see wether these assignments are meaningful based on your chemical knowledge.
Kind regards,
Pengfei
> On Jun 29, 2017, at 8:12 PM, Rana Rehan Khalid <rrkhalid.umich.edu> wrote:
>
> antechamber -fi pdb -fo mol2 -i HEM_H_renum.pdb -o HEM.mol2 -pf y
>
> Info: Bond types are assigned for valence state 9 with penalty of 2
>
> WARNING: atom type of CHD (cf) and C4C (cc) may be wrong
> WARNING: atom type of C2A (cc) and C3A (cc) may be wrong
>
> On Thu, Jun 29, 2017 at 9:07 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
>> antechamber -fi pdb -fo mol2 -i HEM_H_renum.pdb -o HEM.mol2 -c bcc -pf y
>> -nc -4
>>
>> Info: Bond types are assigned for valence state 9 with penalty of 2
>>
>> WARNING: atom type of CHD (cf) and C4C (cc) may be wrong
>> WARNING: atom type of C2A (cc) and C3A (cc) may be wrongTotal number
>> of electrons: 314; net charge: -4
>>
>>
>>
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Received on Fri Jun 30 2017 - 14:00:02 PDT
