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
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Received on Sun Mar 09 2014 - 03:00:03 PDT
