Re: [AMBER] Glycophosphate parametrization using GLYCAM

From: Thomas Pochapsky <>
Date: Wed, 18 Jun 2014 14:15:10 -0400

Sorry, please ignore that message, not intended for AMBER users.


On Jun 18, 2014, at 2:13 PM, Thomas Pochapsky wrote:

> 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.
> T
> 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

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Received on Wed Jun 18 2014 - 11:30:04 PDT
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