VMD-L Mailing List

From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Sat Aug 07 2021 - 18:20:43 CDT

Dear all

 

After using following command  for make HMR

 

if {1} {

package require psfgen

resetpsf ; # Reseteando el psfgen file

readpsf wt_150mM.psf

#coordpdb wt_150mM.pdb

}

 

 

#;## Hydrogen mass repartition command

hmassrepart

writepsf wt_150mM.hmr.psf

quit

 

Get following error too

 

Get following error

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR OH1 H OH1 (ATOMS 3124 3125 3124)

FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR OH1 H OH1 (ATOMS 3124 3125 3124)

 

  

--
Ropón-Palacios G. BSc., MSc. 
Computational biophysicist, 
Associate Research, 
Laboratorio de Modelagem Computacional, 
Departamento de Ciências Exatas, 
Universidad Federal de Alfenas, Minas Gerais, Brasil. 
Phone: +51 935 055240. 
E-mail: groponp_at_gmail.com. 
 
 
 
 
 
From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of "Gumbart, JC" <gumbart_at_physics.gatech.edu>
Date: Saturday, August 7, 2021 at 6:09 PM
To: René Hafner TUK <hamburge_at_physik.uni-kl.de>
Cc: vmd-l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Hydrogen mass repartition PSFGen2.0 
 
 But as always, CHECK the output for correctness! :)
Sage advice!  :) 
 
There’s also a refined approach out there that might be worth a look:  
https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acs.jctc.1c00185__;!!DZ3fjg!vsZDtSouurOnGGiMSYrGiz0DYcCKDmCt7pMuQ57oHHDslu1RltdZZ60DZDjZkLtEZg$ 
 
Best,
JC
 
On Aug 7, 2021, at 4:21 PM, René Hafner TUK <hamburge_at_physik.uni-kl.de> wrote:
 
Hi Ropon,
check the supplemental of this paper https://urldefense.com/v3/__https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.9b00160__;!!DZ3fjg!vsZDtSouurOnGGiMSYrGiz0DYcCKDmCt7pMuQ57oHHDslu1RltdZZ60DZDgNaQx6dA$  .
https://urldefense.com/v3/__https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.9b00160/suppl_file/ct9b00160_si_002.txt__;!!DZ3fjg!vsZDtSouurOnGGiMSYrGiz0DYcCKDmCt7pMuQ57oHHDslu1RltdZZ60DZDgJzOLNXg$ 
 But as always, CHECK the output for correctness! :)
Like the cmd-line tool grep is your friend (or editor of your choice).
Best
René
 
On 8/7/2021 9:57 PM, Ropon-Palacios G. wrote:
Can share me tcl script for make right HMR , please. 
 
 
--
Ropón-Palacios G. BSc., MSc. 
Computational biophysicist, 
Associate Research, 
Laboratorio de Modelagem Computacional, 
Departamento de Ciências Exatas, 
Universidad Federal de Alfenas, Minas Gerais, Brasil. 
Phone: +51 935 055240. 
E-mail: groponp_at_gmail.com. 
 
 
 
 
 
From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of René Hafner TUK <hamburge_at_physik.uni-kl.de>
Date: Saturday, August 7, 2021 at 2:50 PM
To: "Geist, Norman" <norman.geist_at_uni-greifswald.de>, vmd-l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Hydrogen mass repartition PSFGen2.0
 
Hi Norman,
    what would the phyiscal meaning of HMR be, if we keep all non-solvent bonds rigid anyway?
Best
René
On 8/7/2021 8:43 PM, Geist, Norman wrote:
No, you should keep rigid bonds to all. What timestep do you use? Have you checked the PSF contains rescaled masses? (easy to see on hydrogen atoms having a mass of 3)
Im using it for all my simulation without any problems. Don't scale the water, only solute.
Bests
Norman Geist
Am Samstag, den 07-08-2021 um 11:20 schrieb René Hafner TUK:
Hi Geo,
    When using HMR you need to apply rigidBonds to water only. The whole point of repartitioning masses is to reduce fast oscillations frequencies (of hydrogen bonds) you would not allow before due to rigidBonds and with HMR let them oscilliate less fast (which allows higher timestep).
Kind regards
René
 
On 8/6/2021 8:52 PM, Ropon-Palacios G. wrote:
Dear user, 
 
I’m using HMR for a protein with glycosilation (N-glycosilation), make HMR using function implement into psfgen 2.0, 
I’ve check rigth patch but when run md simulation (minimization, equlibration good), get error in rattle algorithm to an hydrogen atoms into atom N involved into glycosilation, as can fix it? 
 
Please help me!. 
 
 
Best, 
 
Geo. 
 
 
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
-- 
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Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany