Warning: DUPLICATE ANGLE/BOND/DIHEDRAL ENTRY FOR ...............

From: Indrajit Deb (biky2004indra_at_gmail.com)
Date: Wed Jun 17 2020 - 00:03:18 CDT

 Hi,
I have prepared my system (protein+dna+rna+nutralizing potassium
ions+water) in CHARMM-GUI and NAMD input files were generated for CHARMM36
parameter sets.

When I am running the NAMD I can see a long list of following warnings on
several duplicate angle/bond/dihedral entries in the NAMD log file.
---------------------------------------------------------------------------------------------

Warning: DUPLICATE ANGLE ENTRY FOR CD-CT2-NH2

PREVIOUS VALUES k=50 theta0=107 k_ub=0 r_ub=0

   USING VALUES k=52 theta0=108 k_ub=0 r_ub=0

Warning: DUPLICATE BOND ENTRY FOR CG331-NG2S3

PREVIOUS VALUES k=266 x0=1.46

   USING VALUES k=255 x0=1.463

Warning: DUPLICATE ANGLE ENTRY FOR NG2R50-NG2R50-NG2R50

PREVIOUS VALUES k=160 theta0=108.2 k_ub=0 r_ub=0

   USING VALUES k=110 theta0=103 k_ub=0 r_ub=0
---------------------------------------------------------------------------------------------

I have tried with commenting out parameter files that are not relevant to
my system (e.g. lipid, carb etc.). Still, the warnings are there. I am
afraid of using the wrong parameters.

The parameter section of the input files looks like below:

# Force-Field Parameters

paraTypeCharmm on; # We're using charmm type
parameter file(s)

                                            # multiple definitions may be
used but only one file per definition

parameters toppar/par_all36_prot.prm

parameters toppar/par_all36_na.prm

parameters toppar/par_all36_carb.prm

parameters toppar/par_all36_lipid.prm

parameters toppar/par_all36_cgenff.prm

parameters toppar/par_interface.prm

parameters toppar/toppar_all36_nano_lig.str

parameters toppar/toppar_all36_nanolig_patch.str

parameters toppar/toppar_all36_synthetic_polymer.str

parameters toppar/toppar_all36_synthetic_polymer_patch.str

parameters toppar/toppar_all36_polymer_solvent.str

parameters toppar/toppar_water_ions.str

parameters toppar/toppar_dum_noble_gases.str

parameters toppar/toppar_ions_won.str

parameters toppar/toppar_all36_prot_arg0.str

parameters toppar/toppar_all36_prot_c36_d_aminoacids.str

parameters toppar/toppar_all36_prot_fluoro_alkanes.str

parameters toppar/toppar_all36_prot_heme.str

parameters toppar/toppar_all36_prot_na_combined.str

parameters toppar/toppar_all36_prot_retinol.str

parameters toppar/toppar_all36_prot_modify_res.str

parameters toppar/toppar_all36_na_nad_ppi.str

parameters toppar/toppar_all36_na_rna_modified.str

parameters toppar/toppar_all36_lipid_bacterial.str

parameters toppar/toppar_all36_lipid_cardiolipin.str

parameters toppar/toppar_all36_lipid_cholesterol.str

parameters toppar/toppar_all36_lipid_dag.str

parameters toppar/toppar_all36_lipid_inositol.str

parameters toppar/toppar_all36_lipid_lps.str

parameters toppar/toppar_all36_lipid_miscellaneous.str

parameters toppar/toppar_all36_lipid_model.str

parameters toppar/toppar_all36_lipid_prot.str

parameters toppar/toppar_all36_lipid_sphingo.str

parameters toppar/toppar_all36_lipid_yeast.str

parameters toppar/toppar_all36_lipid_hmmm.str

parameters toppar/toppar_all36_lipid_detergent.str

parameters toppar/toppar_all36_lipid_ether.str

parameters toppar/toppar_all36_carb_glycolipid.str

parameters toppar/toppar_all36_carb_glycopeptide.str

parameters toppar/toppar_all36_carb_imlab.str

parameters toppar/toppar_all36_label_spin.str

parameters toppar/toppar_all36_label_fluorophore.str

Can anyone please shed light on this issue?

Thanks
Indrajit
--------------------------------------------------------------------------------------------------------------
Indrajit Deb
Postdoctoral Researcher
*https://sites.lsa.umich.edu/frank-lab/
<https://sites.lsa.umich.edu/frank-lab/>*
Department of Biophysics (Room - 3004)
University of Michigan
930 N University Avenue
Ann Arbor, Michigan - 48109, USA
Alternate emails: indrajitdeb81_at_gmail.com, idbmbg_s_at_caluniv.ac.in,
ideb_at_umich.edu
Mobile: +17343588364

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