VMD-L Mailing List

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Wed Jul 13 2022 - 12:43:56 CDT

BINGO !

Dear Pawel,

You managed to notice something so simple and yet so important for my
calculations: A SPACE AFTER THE BACKSLASH!!

After removing those spaces the Cafe 1.0 plugin seems to work correctly.

Thank you so much.

Best regards.

Denilson.

Em qua., 13 de jul. de 2022 às 06:09, Paweł Kędzierski <
pawel.kedzierski_at_pwr.edu.pl> escreveu:

> Dear Denilson,
>
> It seems to me that it is not the fault of the cafe plugin, but something
> preventing the recognition of the backslashes as the line continuation mark.
> The messages 'invalid command name "-trj"' are from the Tcl interpreter,
> and the mmpbsa command is not getting the mandatory "-trj" argument so it
> displays the help and quits.
> Perhaps the file arquivo.tcl has space(s) after the "\", or that it has
> wrong end-of-line format (Unix vs Windows vs MacOS).
> HTH,
> Paweł
>
> W dniu 13.07.2022 o 09:40, DENILSON FERREIRA DE OLIVEIRA pisze:
>
> 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!7MG_ZIV-GNO1m2udlxO4_QcvW1sN4sM3W8_xncy-ksOOOAtWnIniMWUtwbVhM45RGwtgAjzEw8Ney6JW0p4$
>> <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
> regulamentos institucionais vigentes.
>
>
> --
> --
> dr inż. Paweł Kędzierski
> tel. +48 71 320 3200
> Instytut Materiałów Zaawansowanych
> Wydział Chemiczny Politechniki Wrocławskiej
>
> 

-- 
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