Razil,
the "charges" of the hydrogen atoms are mixed into the charges of the
heavy atoms of the chain.
You can also have a look at the supplement of our paper
(10.1038/s41598-018-23624-8), were the charge derivation for a perhaps
similar case is described in some detail.
Maybe that helps.
Regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 11/13/2021 07:37 AM, Razil Tahir wrote:
> Hi Dr,
>
> I have a question regarding the RED program. When we assign the Hydrogen atoms at the acyl tail of the glycolipid molecule to zero, where do the charges of the hydrogen distributed to? To make total charge of the molecule is zero, the charges of the hydrogen atoms must be distributed to other atoms to neutralize the molecule, right?
>
> Thank you in advance.
>
> Razil.
>
> Get Outlook for Android<https://aka.ms/AAb9ysg>
> ________________________________
> From: ABEL Stephane <Stephane.ABEL.cea.fr>
> Sent: Wednesday, July 28, 2021 12:28:05 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
>
> Hi Razil,
>
>>> 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?
> The charge constraints to 0 were applied during the charge fitting and you have to do it manually since REDserver does not do this automatically. To do this you have to use the intramolecular charge constraint keyword : INTRA-MCC applied to the H atoms as described in the REDserver tutorials *
>
> * https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#5
>
> Best
>
> 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 : mardi 27 juillet 2021 16:42
> À : AMBER Mailing List
> Objet : Re: [AMBER] Building Forcefield for Glycolipid Molecule
>
> 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 Mon Nov 15 2021 - 03:30:02 PST
