VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 12 2022 - 17:19:33 CDT

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://github.com/huiliucode/cafe_plugin

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/