Re: [AMBER] on antechamber of AMBER

From: Brett <>
Date: Mon, 2 May 2016 23:01:13 +0800 (CST)

Dear David,

I just read the tutorial in "". In this web page, I do not find it has used

-nc flag for giving the net charges. On the contrary, there is a sentence "Allowing
antechamber to calculate charges and atom types automatically for us using GAFF
allows it to be included in shell scripts that process a large number of

Thus, suppose my compound has a net charge of -3, will you please tell me me the antechamber command to produce mol2 files (or other files) so that antechamber will know the net charge is -3?


At 2016-05-02 22:25:30, "David A Case" <> wrote:
>On Mon, May 02, 2016, Brett wrote:
>> When I read the AMBER on-line tutorial on antechamber (the Sustiva
>> example), I find the antechamber will determine the value of the
>> charge of the ligand.
>This is not true: can you say exactly where in the tutorial you got that
>impression? You must tell antechamber the net charge of the molecule, unless
>it is neutral (which is the default).
>> But for some ligand, for example ADP (adenosine
>> phosphate), if the H has been added by pdbtools (phenix), it will
>> contain -3 charges. But if the H has been added by chimera, it will
>> contain -2 charges. For antechamber, do I nee to add the H before I get
>> the mol2 file by antechamber? And how many charges antechamber will give
>> for ADP?
>You must indeed add hydrogens before running antechamber. The net charge
>that you use (via the -nc flag) depends on how many hydrogens have been added.
>There is often no one "correct" answer, especially for phosphates, which
>generally exist in more than one protonation state near neutral pH.
>AMBER mailing list
AMBER mailing list
Received on Mon May 02 2016 - 08:30:02 PDT
Custom Search