Hi!

Off the top of my head, you have three options.  I'll let you decide which is less painful.

1.  Make yourself a new PGA-like residue, call it whatever you like (999, XYZ, etc.).  It's just like PGA, but it includes O1.  To simplify construction of this residue, try starting with the 1GA residue - to get the internal coordinates right - then remove hydrogens as needed and adjust oxygen charges to match those in PGA.

2.  Make yourself a new SO3-like residue that contains the O1.  Again, call it whatever.  Base it off of the OME residue for angles and torsions, but use bond-lengths that are more appropriate for SO3.  Put this residue first in the file for more ease using leap, but you can eventually manage a build if it is elsewhere.  

3.  Start with 1GA there in leap and manually remove hydrogens and adjust charges and set heads and tails and add all the surrounding residues manually.  Then, build up the rest as it pleases you.  This version might get tricky if you are trying to load a PDB structure rather than trying to create the structure from templates in tleap.  But, it should be possible.

If any of that didn't make sense or needs more explanation, just say.


On Mon, Sep 3, 2018 at 3:45 AM Mohit Chhabra <[log in to unmask]> wrote:

Hi,

 

I have replaced hydroxy at the anomeric position to Sulfate and able to adjust the charges. I have difficulty with the residue name. My first sugar is PGB (PDB file is attached for your perusal).  Glycam06j_1 doesn't include O1 in the PGB residue. How should I name the residue consisting of oxygen "O1" that is linked to PGB?

 

Regards

Mohit

 

 

Sent from Mail for Windows 10

 


From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Lachele Foley <[log in to unmask]>
Sent: Wednesday, June 13, 2018 11:23:53 PM
To: [log in to unmask]
Subject: Re: ADD PHOSPHATE DERIVATIVE
 
Which residue are you starting with?

If you haven't seen these instructions, they might help:  




On Tue, Jun 12, 2018 at 9:48 PM, Xiaocong Wang <[log in to unmask]> wrote:

Hi Neha,

We haven't tested phosphate charges explicitly, that's why we haven't released charges for phosphate on our webtool.

Best,

Xiao


Xiaocong Wang
Complex Carbohydrate Research Center
The University of Georgia
Tel: (706) 254-7958

From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Neha S. Gandhi <[log in to unmask]>
Sent: Tuesday, June 12, 2018 8:41:36 PM

To: [log in to unmask]
Subject: Re: ADD PHOSPHATE DERIVATIVE
 

Hi Lachele,

 

Mohit works with me, and he is acquainted using tleap in AMBER.

 

If I remember the charge correctly on anomeric position (OH) is -0.194. If we add sulphate at this position, how are the charges taken into account at the anomeric position?

 

GLYCAM has parameters for phosphate but not the charges.

 

Many thanks,

Neha

 

From: Users of GLYCAM & GLYCAM-Web [mailto:[log in to unmask]] On Behalf Of Lachele Foley
Sent: Wednesday, 13 June 2018 12:32 AM
To: [log in to unmask]
Subject: Re: ADD PHOSPHATE DERIVATIVE

 

Just to be sure I understand:  You want to sulfate the monosaccharide at all positions including the anomeric position?   You can't do that with the builder, but it can be done using tleap.  Are you familiar with tleap?

 

I don't recall the status of the phosphate derivative development, but it isn't ready.  Anyone know the status?  

 

 

On Tue, Jun 12, 2018 at 10:14 AM, Mohit Chhabra <[log in to unmask]> wrote:

Hi,

I have a 5-sugar units chain in my molecule and I want to substitute sulfate at all the positions but when I try to add sulfate as a derivative on the end terminal sugar, it always gives free OH at position 1 of sugar using "carbohydrate builder” option. If I download that file and add sulfate by replacing OH, the charge of sulfate will still be +0.194 as it was of OH but the charge of sulfate should be same as of other sulfates. If there is any possible way to design a fully sulfated carbohydrate, please suggest.

Also, I would like to add phosphate at the 6th position of mannose by replacing sulfate but couldn't add phosphate as derivative. There is an option to add phosphate as a derivative but it's not functioning. Please suggest what can be the possible way to do that or how the charges of phosphate can be derived.

Regards
Mohit



 

--

:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA




--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA


--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA