VMD-L Mailing List

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Wed Jul 13 2022 - 02:40:55 CDT

OK.

Thanks.

Best regards.

Denilson.

Em ter., 12 de jul. de 2022 às 19:19, John Stone <johns_at_ks.uiuc.edu>
escreveu:

> Hi,
> It looks like would be something best asked by posting an issue on the
> CaFE github? Maybe you can get the authors' attention?:
> https://urldefense.com/v3/__https://github.com/huiliucode/cafe_plugin__;!!DZ3fjg!-uQzXoF-x0hrM8z133oMjPhegyeUipl6lOTO35VYNU-LmmXCzt4ZaWv0XK54v1vTC4_J5yNvDQTVLx2bxdE$
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jul 11, 2022 at 11:07:19AM -0300, DENILSON FERREIRA DE OLIVEIRA
> wrote:
> > Dear all,
> >
> > *1) In order to use Cafe 1.0 to carry out MMPBSA calculations I used the
> > following command:*
> >
> > /programas/vmd_1.9.4a55/bin/vmd_1.9.4a55 -dispdev text -eofexit <
> > arquivo.tcl > arquivo.log
> >
> > *2) The contents of the file "arquivo.tcl" are transcribed below:*
> >
> > package require cafe 1.0
> >
> > mmpbsa -top A1_ERGH-S-11-001.psf \
> > -trj A1_ERGH-S-11-005.dcd \
> > -out A1_ERGH-S-11-005.log \
> > -par par_all36m_prot.prm \
> > -par par_all36_lipid.prm \
> > -par par_all36_carb.prm \
> > -par par_all36_na.prm \
> > -par par_all36_cgenff.prm \
> > -par toppar_all36_carb_glycopeptide.str \
> > -par toppar_water_ions_namd.str \
> > -par A1_ERGH-S-11-chi-COR.str \
> > -com "segname AP1 BP1 CP1 AG1 AG2 AG3 AG4 AG5 AG6 AG7 AG8 AG9 AG10
> > AG11 AG12 AG13 AG14 AG15 AG16 BG1 BG2 BG3 BG4 BG5 BG6 BG7 BG8 BG9 BG10
> BG11
> > BG12 BG13 BG14 BG15 BG16 CG1 CG2 CG3 CG4 CG5 CG6 CG7 CG8 CG9 CG10 CG11
> CG12
> > CG13 CG14 CG15 CG16 ZO1" \
> > -rec "segname AP1 BP1 CP1 AG1 AG2 AG3 AG4 AG5 AG6 AG7 AG8 AG9
> AG10
> > AG11 AG12 AG13 AG14 AG15 AG16 BG1 BG2 BG3 BG4 BG5 BG6 BG7 BG8 BG9 BG10
> BG11
> > BG12 BG13 BG14 BG15 BG16 CG1 CG2 CG3 CG4 CG5 CG6 CG7 CG8 CG9 CG10 CG11
> CG12
> > CG13 CG14 CG15 CG16" \
> > -lig "segname ZO1" \
> > -first 900 \
> > -last -1 \
> > -stride 1 \
> > -mm 1 \
> > -mm_exe namd2 \
> > -mm_diel 1.0 \
> > -pb 2 \
> > -pb_exe apbs \
> > -pb_rad mparse \
> > -pb_indi 1.0 \
> > -pb_exdi 80.0 \
> > -pb_scale 2.0 \
> > -pb_perfil 80.0 \
> > -pb_perbrad 1.4 \
> > -pb_linit 1000 \
> > -pb_maxc 0.0001 \
> > -pb_bcfl mdh \
> > -pb_chgm sp12 \
> > -pb_srfm smol \
> > -pb_swin 0.3 \
> > -pb_sdens 10.0 \
> > -sa 1 \
> > -sa_rad mparse \
> > -sa_gamma 0.00542 \
> > -sa_beta 0.92 \
> > -sa_prbrad 1.4 \
> > -sa_samples 500
> >
> > quit
> >
> >
> > *3) The contents of the file "arquivo.log" are transcribed below:*
> > Info) VMD for LINUXAMD64, version 1.9.4a55 (October 18, 2021)
> > Info) http://www.ks.uiuc.edu/Research/vmd/
> > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > Info) Please include this reference in published work using VMD:
> > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > Info) -------------------------------------------------------------
> > Info) Multithreading available, 8 CPUs, ISA dispatch enabled.
> > Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
> > Info) Free system memory: 29GB (91%)
> > Info) No CUDA accelerator devices available.
> > Info) Dynamically loaded 3 plugins in directory:
> > Info) /programas/vmd_1.9.4a55/plugins/LINUXAMD64/molfile
> > 1.0
> > CaFE) Sanity check
> > CaFE) Usage: mmpbsa -top filename -trj filename [-args...]
> > CaFE) Mandatory arguments:
> > CaFE) -top <topology filename>
> > CaFE) -trj <trajectory filename>
> > CaFE) Optional arguments:
> > CaFE) -top_type <topology filetype> -- default: auto
> > CaFE) -trj_type <trajectory filetype> -- default: auto
> > CaFE) -par <force field parameters> -- default:
> > /programas/vmd_1.9.4a55/plugins/noarch/tcl/cafe1.0/par_all22_prot.inp
> > CaFE) -out <output filename> -- default: result.log
> > CaFE) -debug <debug level> -- default: 0
> > CaFE) -first <first frame> -- default: 0
> > CaFE) -last <last frame> -- default: -1
> > CaFE) -stride <stride> -- default: 1
> > CaFE) -com <complex selection> -- default: ""
> > CaFE) -rec <receptor selection> -- default: ""
> > CaFE) -lig <ligand selection> -- default: ""
> > CaFE) -mm <do gas-phase calculation> -- default: 0
> > CaFE) -mm_exe <path to NAMD> -- default: "namd2"
> > CaFE) -mm_diel <dielectric constant> -- default: 1.0
> > CaFE) -pb <do PB calculation> -- default: 0
> > CaFE) -pb_exe <path to DelPhi/APBS> -- default: "delphi77"
> > CaFE) -pb_siz <radii parameter file> -- default: ""
> > CaFE) -pb_crg <charge parameter file> -- default: ""
> > CaFE) -pb_rad <type of PB radii> -- default: bondi
> > CaFE) -pb_indi <internal dielectric> -- default: 1.0
> > CaFE) -pb_exdi <external dielectric> -- default: 80.0
> > CaFE) -pb_scale <scale> -- default: 2.0
> > CaFE) -pb_perfil <percentage of fill> -- default: 80.0
> > CaFE) -pb_prbrad <radius of probe> -- default: 1.4
> > CaFE) -pb_linit <linear iterations> -- default: 1000
> > CaFE) -pb_maxc <convergence threshold> -- default: 0.0001
> > CaFE) -pb_bndcon <boundary condition> -- default: 4
> > CaFE) -pb_bcfl <boundary condition> -- default: sdh
> > CaFE) -pb_chgm <charge method> -- default: spl0
> > CaFE) -pb_srfm <surface method> -- default: smol
> > CaFE) -pb_swin <spline window width> -- default: 0.3
> > CaFE) -pb_sdens <number of grids> -- default: 10.0
> > CaFE) -gb <do GB calculation> -- default: 0
> > CaFE) -gb_exdi <external dielectric> -- default: 78.5
> > CaFE) -gb_ioncon <ion concentration> -- default: 0.0
> > CaFE) -gb_sa <do LCPO calculation> -- default: 0
> > CaFE) -gb_sagamma <surface tension> -- default: 0.005
> > CaFE) -sa <do SA calculation> -- default: 0
> > CaFE) -sa_exe <path to APBS> -- default: "apbs"
> > CaFE) -sa_rad <type of SA radii> -- default: bondi
> > CaFE) -sa_gamma <surface tension> -- default: 0.005
> > CaFE) -sa_beta <surface offset> -- default: 0.0
> > CaFE) -sa_prbrad <radius of probe> -- default: 1.4
> > CaFE) -sa_samples <number of samples> -- default: 500
> > invalid command name "-trj"
> > invalid command name "-out"
> > invalid command name "-par"
> > invalid command name "-par"
> > invalid command name "-par"
> > invalid command name "-par"
> > invalid command name "-par"
> > invalid command name "-par"
> > invalid command name "-par"
> > invalid command name "-par"
> > invalid command name "-com"
> > invalid command name "-rec"
> > invalid command name "-lig"
> > invalid command name "-first"
> > invalid command name "-last"
> > invalid command name "-stride"
> > invalid command name "-mm"
> > invalid command name "-mm_exe"
> > invalid command name "-mm_diel"
> > invalid command name "-pb"
> > invalid command name "-pb_exe"
> > invalid command name "-pb_rad"
> > invalid command name "-pb_indi"
> > invalid command name "-pb_exdi"
> > invalid command name "-pb_scale"
> > invalid command name "-pb_perfil"
> > invalid command name "-pb_perbrad"
> > invalid command name "-pb_linit"
> > invalid command name "-pb_maxc"
> > invalid command name "-pb_bcfl"
> > invalid command name "-pb_chgm"
> > invalid command name "-pb_srfm"
> > invalid command name "-pb_swin"
> > invalid command name "-pb_sdens"
> > invalid command name "-sa"
> > invalid command name "-sa_rad"
> > invalid command name "-sa_gamma"
> > invalid command name "-sa_beta"
> > invalid command name "-sa_prbrad"
> > invalid command name "-sa_samples"
> > Info) VMD for LINUXAMD64, version 1.9.4a55 (October 18, 2021)
> > Info) Exiting normally.
> >
> > *4) For some reason the CAFE plugin is not recognizing the commands.*
> >
> > I would appreciate it if anyone could be kind enough to help me to solve
> > the problem.
> >
> > Denilson.
> >
> > --
> > Dr. Denilson F. Oliveira
> > Professor Titular
> > Laboratório de Produtos Naturais
> > Departamento de Química
> > Universidade Federal de Lavras
> > Caixa Postal 3037
> > Lavras-MG-Brasil
> > CEP 37.200-900
> > Tel: (55) (35) 3829-1623
> > e-mail: denilson_at_ufla.br
> >
> > --
> > O conteúdo deste e-mail e anexos são restritos aos seus destinatários e
> de
> > responsabilidade do remetente. O uso do e-mail deve estar de acordo com
> os
> > regulamentos institucionais vigentes.
>
>
> --
> Research Affiliate, NIH Center for Macromolecular Modeling and
> Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
O conteúdo deste e-mail e anexos são restritos aos seus destinatários e de 
responsabilidade do remetente. O uso do e-mail deve estar de acordo com os 
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