I believe the issue is here:
Loading Prep file: ./singleMaltose.prepin
Starting with version 06h, the naming convention for glycan atom types
is capital-lower. So, the atom types in your singleMaltose.prepin
file need to follow this convention. That is, Os, not OS. Also Cg,
not CG, and so forth.
On Thu, Sep 11, 2014 at 9:59 AM, Vijyan Achari <vjrajamani.yahoo.co.uk> wrote:
> I am trying to setting up topology file for maltoside (with two glucose sugars).
>
> I used command "tleap -f maltose.input" and the file 'maltose.input' contains info such as:
>
> source leaprc.GLYCAM_06j-1
>
> source leaprc.ff12SB
>
> source leaprc.lipid14
> loadamberprep singleMaltose.prepin
>
> mol = loadpdb singleMaltose.pdb
>
> check mol
>
>
>
> Once I run above I get message as below:
>
>
> vijay.ramana:~/Simulation_projects/Selvi-project/1-preparation$ tleap -f vjnew-betaMaltose
> -I: Adding /usr/local/apps/amber14/dat/leap/prep to search path.
> -I: Adding /usr/local/apps/amber14/dat/leap/lib to search path.
> -I: Adding /usr/local/apps/amber14/dat/leap/parm to search path.
> -I: Adding /usr/local/apps/amber14/dat/leap/cmd to search path.
> -f: Source vjnew-betaMaltose.
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: ./vjnew-betaMaltose
> ----- Source: /usr/local/apps/amber14/dat/leap/cmd/leaprc.GLYCAM_06j-1
> ----- Source of /usr/local/apps/amber14/dat/leap/cmd/leaprc.GLYCAM_06j-1 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: /usr/local/apps/amber14/dat/leap/prep/GLYCAM_06j-1.prep
> Loading library: /usr/local/apps/amber14/dat/leap/lib/GLYCAM_amino_06j_12SB.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/GLYCAM_aminoct_06j_12SB.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/GLYCAM_aminont_06j_12SB.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/solvents.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/atomic_ions.lib
> Loading parameters: /usr/local/apps/amber14/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)
> ----- Source: /usr/local/apps/amber14/dat/leap/cmd/leaprc.ff12SB
> ----- Source of /usr/local/apps/amber14/dat/leap/cmd/leaprc.ff12SB done
> Log file: ./leap.log
> Loading parameters: /usr/local/apps/amber14/dat/leap/parm/parm10.dat
> Reading title:
> PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> Loading parameters: /usr/local/apps/amber14/dat/leap/parm/frcmod.ff12SB
> Reading force field modification type file (frcmod)
> Reading title:
> ff12SB protein backbone and sidechain parameters
> Loading library: /usr/local/apps/amber14/dat/leap/lib/amino12.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/aminoct12.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/aminont12.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/nucleic12.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/atomic_ions.lib
> Loading library: /usr/local/apps/amber14/dat/leap/lib/solvents.lib
> Substituting map 0HYP -> HYP for 0HYP -> NHYP
> Substituting map 1HYP -> CHYP for 1HYP -> CHYP
> ----- Source: /usr/local/apps/amber14/dat/leap/cmd/leaprc.lipid14
> ----- Source of /usr/local/apps/amber14/dat/leap/cmd/leaprc.lipid14 done
> Log file: ./leap.log
> Loading parameters: /usr/local/apps/amber14/dat/leap/parm/lipid14.dat
> Reading title:
> AMBER Lipid14 Force Field, C. Dickson, B. Madej, A.Skjevik, K. Teigen, I.R. Gould, R.C. Walker*
> Loading library: /usr/local/apps/amber14/dat/leap/lib/lipid14.lib
> Loading Prep file: ./singleMaltose.prepin
>
> Loading PDB file: ./singleMaltose.pdb
> total atoms in file: 81
> Checking 'mol'....
> Checking parameters for unit 'mol'.
> Checking for bond parameters.
> Could not find bond parameter for: OS - Cg
> Could not find bond parameter for: Cg - OS
> Could not find bond parameter for: OS - Cg
> Could not find bond parameter for: Cg - OS
> Could not find bond parameter for: OS - Cg
> Could not find bond parameter for: Cg - OS
> Checking for angle parameters.
> Could not find angle parameter: OS - Cg - H2
> Could not find angle parameter: OS - Cg - Os
> Could not find angle parameter: Cg - Cg - OS
> Could not find angle parameter: H1 - Cg - OS
> Could not find angle parameter: Cg - OS - Cg
> Could not find angle parameter: Cg - Cg - OS
> Could not find angle parameter: Cg - Cg - OS
> Could not find angle parameter: OS - Cg - Cg
> Could not find angle parameter: OS - Cg - H1
> Could not find angle parameter: OS - Cg - Cg
> Could not find angle parameter: H2 - Cg - OS
> Could not find angle parameter: Cg - OS - Cg
> Could not find angle parameter: OS - Cg - H2
> Could not find angle parameter: OS - Cg - OS
> Could not find angle parameter: Cg - Cg - OS
> Could not find angle parameter: H1 - Cg - OS
> Could not find angle parameter: Cg - OS - Cg
> Could not find angle parameter: Cg - Cg - OS
> Could not find angle parameter: Cg - Cg - OS
> Could not find angle parameter: Cg - Cg - OS
> There are missing parameters.
> Unit is OK.
>>
>
> May I know what went wrong here?
>
> Regards
> Vijay
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 11 2014 - 07:30:04 PDT
