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
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Received on Thu Sep 11 2014 - 07:30:03 PDT
