Just to follow up on this: The main issues were with atom type
assignments. They were compounded by trying to use version GLYCAM_06j
with ff99SB. Once the typing issues were corrected, and ff12SB was
used instead, it built fine.
I suggested, also, trying the lipid force field rather than one for
proteins and nucleic acids. That will require assignment of a small
number of parameters for the linkage. I suggested the following.
Other devs, particularly Ross, might want to weigh in. I said to use
glycam parameters for anything mostly on the glycan side or that
centers on the glycosidic oxygen (I saw only one angle like the latter
on the list of missing parms). Use the lipid params for anything that
is mostly on the lipid side. And... test it well.
On Sun, Mar 9, 2014 at 5:37 AM, Vijay Manickam Achari
<vjrajamany.yahoo.com> wrote:
> Thanks for the reply sir.
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
>
>
>
> On Saturday, 8 March 2014, 20:45, ABEL Stephane 175950 <Stephane.ABEL.cea.fr> wrote:
>
> Hello,
>
> Previously, we derived RESP charges for a alkyl-glycosides molecules. See you paper :
>
> http://pubs.acs.org/doi/full/10.1021/jp109545v
>
> and the associated RED project : http://q4md-forcefieldtools.org/REDDB/projects/F-72/ where the parameters are stored. You will find the input file for LEaP!
>
> HTH
>
>
> --------
> Stéphane Abel, PhD
> CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> Bat 528 Room 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : Vijay Manickam Achari [vjrajamany.yahoo.com]
> Envoyé : samedi 8 mars 2014 11:29
> À : Amber mailing List
> Cc : vjachari.gmail.com
> Objet : [AMBER] modeling glucoside
>
> I am trying to model glucoside. In this molecule I have a glucose (sugar) and alkyl chain with 8 carbons.
>
> I prepared the "Glucoside.prepin" file using antechamber.
> I loaded GLYCAM_06j.dat and leaprc.GLYCAM_06j files with xleap.
>
>
> The sugar headgroup do not give any warning.
>
>
> But when I assigned the "atom type" for alkyl chain carbons to be "CT" and for the hydrogen connected to this carbons to be "HC". When I load this molecule and associate prepin file into xleap, I get message something below.
>
>
>
>
> The warning I get is below:
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: ./vjnew-Octyl-Osama.xleap
> ----- Source: ./leaprc.GLYCAM_06j
> ----- Source of ./leaprc.GLYCAM_06j done
> Loading parameters: ./GLYCAM_06j.dat
> Reading title:
> GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
> Loading Prep file: ./GLYCAM_06j.prep
> Loading library: ./GLYCAM_amino_06j_10.lib
> Loading library: ./GLYCAM_aminoct_06j_10.lib
> Loading library: ./GLYCAM_aminont_06j_10.lib
> Loading library: /usr/local/apps/amber12/dat/leap/lib/solvents.lib
> Loading library: /usr/local/apps/amber12/dat/leap/lib/ions08.lib
> Loading parameters: /usr/local/apps/amber12/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
> Loading parameters: ./GLYCAM_06j.dat
> Reading title:
> GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
> Loading Prep file: ./octylGluco.prepin
>> gg=loadpdb octylGluco.pdb
> Loading PDB file: ./octylGluco.pdb
> total atoms in file: 48
>> check gg
> Checking 'gg'....
> Checking parameters for unit 'gg'.
> Checking for bond parameters.
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - CT
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - CT
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - CT
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - CT
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - CT
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - CT
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - HC
> Could not find bond parameter for: CT - CT
> Checking for angle parameters.
> Could not find angle parameter: HC - CT - Os
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - Os
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - CT
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - HC
> Could not find angle parameter: HC - CT - CT
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - HC
> Could not find angle parameter: CT - CT - CT
> There are missing parameters.
> Unit is OK.
>
>
>
> I need to know what "atom type" should I use for the alkyl chain?
>
>
> I appreciate if get some help here.
>
> Many thanks in advnace.
>
> Vijay Manickam Achari
>
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of
> Malaya,
> Malaysia
> vjramana.gmail.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Mar 14 2014 - 09:00:03 PDT
