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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