QwikMD Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Jun 28 2018 - 10:34:17 CDT

When I run the generated scripts from QwikMD, I notice in the log file this:

 PARAMETER file: CHARMM format!
Info: PARAMETERS toppar_all36_na_nad_ppi_gdp_gtp_qwikmd.str
Info: PARAMETERS toppar_water_ions_namd.str
Info: PARAMETERS toppar_all36_carb_glycopeptide.str
Info: PARAMETERS par_all36_lipid.prm
Info: PARAMETERS par_all36_na.prm
Info: PARAMETERS par_all36_prot.prm
Info: PARAMETERS par_all36_carb.prm
Info: PARAMETERS par_all36_cgenff.prm
Info: PARAMETERS AMTMitch_qwikmd.str
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE

The total charge is specified in the RTF, but does "SKIPPING rtf SECTION IN STREAM FILE" also skip the
charge specification? Or does NAMD use the charges in the PSF file and it adds up those charges to the
total charge? I ask because my ligand is a +1 charge, and it needs to be +1 during the simulation. The partial
charges add up to +1, but does NAMD use the total charge from the RTF or the partial charges from the PSF? Thanks!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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