Re: [AMBER] bond missing in phosphate group after antechamber run

From: Krisztina Feher <>
Date: Thu, 8 Nov 2012 08:55:45 -0800 (PST)

Thanks a lot for looking at my pdb file, David!

Regarding the pdb format, I implemented all your suggestions, but there are still two atoms that are not recognised by antechamber: the deoxy-ribose have H2' and H2'' as well as H5' and H5'', but the two prime notations are always changed by antechamber to H9 and H10 and the atom type is assiged DU (see attached), which means antechamber could not recognise it... What shall I do with them?

Regarding the sense of the protonation state: without the H caps on the phosphate group antechamber was complaining about open valences. Question: How one can use an ionised phosphate group with antechamber? With counter ions?


--- On Thu, 11/8/12, David A Case <> wrote:

From: David A Case <>
Subject: Re: [AMBER] bond missing in phosphate group after antechamber run
To: "AMBER Mailing List" <>
Date: Thursday, November 8, 2012, 3:56 PM

On Wed, Nov 07, 2012, Krisztina Feher wrote:
> I am trying to derive GAFF parameters for a modified DNA residue with
> antechamber. I capped the residue with H's and ran through antechamber
> and parmcheck without error. However the bond between the oxigen and
> phosphorus is missing in the mol2 file as well as the respective
> parameters in the .frcmod file. Could someone have a look at teh input
> pdb file for antechamber to figure out the reason for this?

Your pdb file is badly formatted.  First, all the atoms should be in the same
residue, but atoms 47-50 are not.  When you put everything in one residue,
make sure the atom names are all unique (you can't have two atoms named "O1",
for example.)

More importantly, atom names in pdb file must be in residues 13-16, and hence
can be at most 4 characters.  You have atom names that are in column 17 (atoms
42-46).  This leads antechamber to change your atom names, since it thinks
you have duplicates.

As an aside: a terminal phosphate group will only be doubly protonated under
extremely acidic conditions.  Unless you are sure you really have what is in
your pdb file, you should probably create a residue library for the -1 or -2
charge state of this molecule.

...good luck...dac

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