Hello Dr,
I have looked at the paper and the supplementary information. Thank you so much for such a great work!
I have a question. In the Table S1 in supplementary information, I saw that in the DOD acyl chain, only the carbon atom has non-zero partial charges, whereas the partial charges for all hydrogen atom are 0. Are these values coming from the RESP calculation or we need assign these zero values manually? Or there are some functions in RED program to help us to do so?
Thank you so much.
Razil
________________________________
From: ABEL Stephane <Stephane.ABEL.cea.fr>
Sent: Wednesday, July 21, 2021 5:35 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Hello,
If you cannot use the CT atom type for your model (without further optimisation) you could use the glycam web server to get the parameters by analogy
http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1
For the RESP charges, as anselm.horn, we used the RED server and followed the GLYCAM philosophy (your could read the SI of our paper too)
HTH
Stéphane
----------------------------------------------------------
Stéphane Abel, Ph.D., HDR
CEA Centre de Saclay
DRF/JOLIOT/I2BC-S/SB2SM/LBMS
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : Razil Tahir [raziltahir.hotmail.com]
Envoyé : mercredi 21 juillet 2021 03:38
À : AMBER Mailing List
Objet : Re: [AMBER] Building Forcefield for Glycolipid Molecule
Hi, Dr.
Thank you for the response.
I've tried to use CT atomtype from the GLYCAM for the acyl chain but when I ran parmchk and generated the frcmod file, there are angles, bonds and dihedral angles that requires attention (ATTN, need revision).
How do you resolve this and where should I refer to get the values?
My next question is why did you choose RESP for the charges?
Thank you, Dr.
Razil.
________________________________
From: ABEL Stephane <Stephane.ABEL.cea.fr>
Sent: Monday, July 19, 2021 4:56 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
Hello
You could take a look of my paper see
1. Abel S, Dupradeau F-YY, Raman EP, MacKerell AD, Marchi M. 2011 Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters. J. Phys. Chem. B 115, 487–499. (doi:10.1021/jp109545v)
I developed RESP charges for glycolipids and used them with GLYCAM parameters
Good luck
Stéphane
________________________________________
De : Razil Tahir [raziltahir.hotmail.com]
Envoyé : dimanche 18 juillet 2021 19:02
À : AMBER Mailing List
Objet : [AMBER] Building Forcefield for Glycolipid Molecule
Hello experts,
I'm currently trying to build a forcefield for a glycolipid molecule. I'm using the GLYCAM forcefield for the sugar headgroup but there's no parameter for the alkyl chain.
I've calculated the partial charges using Gaussian09 and took the parameters for the alkyl chain from the GAFF forcefield.
Is this method practical and correct to be used? Please advise.
Thank you.
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Received on Tue Jul 27 2021 - 08:00:02 PDT
