On 08/24/2013 06:17 PM, David Case wrote:
>
>
> On Aug 24, 2013, at 9:44 AM, "Barnett, James W." <jbarnet4.tulane.edu> wrote:
>>
>> I've read some in the mailing list and manual that pdb files should have
>> "all hydrogens" for use with antechamber. I believe this is addressing
>> the issue that some protein files don't have all of them when retrieved
>> from a database (i.e., antechamber doesn't assume hydrogens are present).
>
> It's hard to understand the above. Antechamber is not ordinarily used for proteins. But it never adds hydrogens so they all need to be there in the input file.
>
I must have just misinterpreted what I was reading in that case.
>>
>> But, I have an organic molecule with a charge of -6. Therefore I have
>> removed six hydrogens at appropriate places in the molecule
>
> Is this what you mean: you want the charge to be -6, but you have a structure where the charge is zero? In that case it would be appropriate to remove 6 hydrogens. Be sure to use the -n flag to tell antechamber what net charge to use.
>
Exactly. Thanks!
--
Wes Barnett | jbarnet4.tulane.edu
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Received on Mon Aug 26 2013 - 07:00:02 PDT
