VMD-L Mailing List

From: DENILSON FERREIRA DE OLIVEIRA (denilson_at_ufla.br)
Date: Mon Jul 11 2022 - 09:07:19 CDT

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
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