Dear GLYCAM users,

I would like to ask you kindly for advice involving incorporation of a protonated beta-D-glucuronic acid parameters into GLYCAM force field. I have noticed that there already are some discussions related to this issue so I have read them throughoutly but it did not help me.

I am using AMBER for simulations of hyaluronic acid dimers and I am not able to incorporate the protonated versions. I have found suitable frcmod and prep files on the GLYCAM website and modified a PDB file generated in the Carbohydrate builder (add the hydrogen and double bonds), but the results are still identical as without incorporating these files – „The file contained 1 atoms not in residue templates.“ I am wondering, where the problem is, whether is it in the PDB file or somewhere else. I am also not sure if AMBER can work with 4-letter residue names (4ZBP). I attach all the files needed including the log file.

Thank you in advance for your responses.

With kind regards,

Pavlína Slavníková

the UCT Prague student





Welcome to LEaP!
(no leaprc in search path)
> source leaprc.GLYCAM_06j-1
----- Source: /software/amber-16/intel/dat/leap/cmd/leaprc.GLYCAM_06j-1
----- Source of /software/amber-16/intel/dat/leap/cmd/leaprc.GLYCAM_06j-1 done
Loading parameters: /software/amber-16/intel/dat/leap/parm/GLYCAM_06j.dat
Reading title:
GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
Loading Prep file: /software/amber-16/intel/dat/leap/prep/GLYCAM_06j-1.prep
Loading library: /software/amber-16/intel/dat/leap/lib/GLYCAM_amino_06j_12SB.lib
Loading library: /software/amber-16/intel/dat/leap/lib/GLYCAM_aminoct_06j_12SB.lib
Loading library: /software/amber-16/intel/dat/leap/lib/GLYCAM_aminont_06j_12SB.lib
Loading library: /software/amber-16/intel/dat/leap/lib/solvents.lib
Loading library: /software/amber-16/intel/dat/leap/lib/atomic_ions.lib
Loading parameters: /software/amber-16/intel/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)
> loadamberparams frcmod.A-NAc
Loading parameters: ./frcmod.A-NAc
Reading force field modification type file (frcmod)
Reading title:
Protonated Beta-D-Glucuronic acid
>
> loadamberprep A-NAc.prep
Loading Prep file: ./A-NAc.prep
> hyal = loadPdb A-NAc_upr.pdb
Loading PDB file: ./A-NAc_upr.pdb
Created a new atom named: H6O within residue: .R<4ZB 2>
  total atoms in file: 50
  The file contained 1 atoms not in residue templates