Re: [AMBER] Glycophosphate parametrization using GLYCAM

From: Lachele Foley <>
Date: Wed, 18 Jun 2014 13:48:44 -0400

You could make yourself a dummy "PO3" residue by substituting atom
names and types from the SO3 residue. You'd still need to set atom
types for the attaching carbon (Cp). After everything is done, you
still need to assign charges. For this, you can hack the topology
file if you feel like it. Or, you can create a prep file for your
molecule as a whole (antechamber) and build a top file from that. If
you choose the latter, you can have leap write out a pdb from using
your fake-PO3 prep and base your new prep file on that. You could
also get a pdb from GLYCAM-Web by building the sulfated analog for
what you want and change the S's to P's. Then, build a prep file from
that (and your new charges, however you generate them). There will be
slight geometry differences between SO3 and PO3, but a minimization
should fix those pretty quickly.

On Wed, Jun 18, 2014 at 5:23 AM, Jochen Heil <> wrote:
> Dear Lachelle and Francois,
> thanks for the quick replies.
> .Lachelle
> I think our main point of confusion is/was the lack of a "PO3" residue
> in the GLYCAM force field files, while there is one for "SO3". We have
> used the AMBER protein force field as well as GAFF in the past, however,
> obviously the usual simple AMBER workflow that we are used to (have a
> PDB file with correct AMBER residue names and let leap assign atom types
> based on residue templates) does not work in our case here. So it seems
> that we need to assign atom types manually and individually for each
> atom using leap's "set" command, like you did in that example.
> .Francois
> "I would vote for splitting each monosaccharide and the phosphate into
> two different building blocks involved in charge derivation..."
> I think this is what we will do. In this case the PO4 moiety should be
> simply reusable with other sugars if we want to play around with these
> later on. However, as far as I understand things, we will need to
> construct several different carbohydrate-phosphates and perform the ESP
> fit process simultaneously for all of them, subject to the constraints that
> -the partial charges of all atoms of the carbohydrate moiety retain
> their original GLYCAM-defined value,
> -the partial charges of all atoms of the phosphate moiety are the same
> for each carbohydrate-phosphate and
> -the sum of the partial charges of the phosphate moiety is equal to the
> integer total charge of the carbohydrate-phosphate minus the sum of the
> partial charges of the carbohydrate moiety. That would mean using inter-
> as well as intramolecular charge constraints in "RED-parlance" and the
> process should be similar to J. Org. Chem. 2007, 72, 9032-9045 by Gouin
> et al and your tutorial "V.4- Force field for a set of glycoconjugate
> fragments", right?
> Best regards,
> Raj Schneider & Jochen Heil,
> TU Dortmund,
> Germany
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Wed Jun 18 2014 - 11:00:03 PDT
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