Re: [AMBER] Glycophosphate parametrization using GLYCAM

From: Thomas Pochapsky <>
Date: Wed, 18 Jun 2014 14:13:31 -0400

Sure, that would be ok. I would be ok with 1 day but as I go over the material, I just realize how much there is.

On Jun 18, 2014, at 1:48 PM, Lachele Foley wrote:

> 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

AMBER mailing list
Received on Wed Jun 18 2014 - 11:30:03 PDT
Custom Search