Re: QwikMD Question

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Jun 28 2018 - 12:08:13 CDT

Hi Kelly,

this information printed by NAMD during the start-up process is to inform
the user that the topology information (rtf section) in the stream files
(*.str) is not used by NAMD. All this information is read from the psf.
This is valid for QwikMD and for any simulation in NAMD that uses stream
files with topology information.

Best

João

On Thu, Jun 28, 2018 at 10:39 AM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> 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*
>
>
>

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851

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