VMD-L Mailing List

From: Artur Hermano (artur.hermano_at_hotmail.com)
Date: Mon Feb 14 2022 - 11:03:59 CST

Hello John and Mike,

thank you very much for the help! I will download the latest version and give it a try then!

Best,
Artur
________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Friday, February 11, 2022 01:03
To: Artur Hermano <artur.hermano_at_hotmail.com>
Cc: CHARLES MCCALLUM <cmccallum_at_me.com>; KS UIUC <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: hmassrepart

Hi,
  You need to be running VMD 1.9.4, or you are not using the current
version of the psfgen plugin. The hydrogen mass repartitioning
feature was added to psfgen late in VMD 1.9.4 development, so you
will need to use a current VMD 1.9.4 test build or a current NAMD nightly
build if you want to use it.

Best,
  John

On Fri, Feb 11, 2022 at 12:25:43AM +0000, Artur Hermano wrote:
> Hey Mike, so I have just checked and my psfgen version is actually 2.0(!!)
> I even tried calling "hmassrepart" within the psfgen interface, but the
> same invalid command error happened, so I just don't know what to do :/
> Best,
> Artur
>
> --------------------------------------------------------------------------
>
> From: CHARLES MCCALLUM <cmccallum_at_me.com>
> Sent: Thursday, February 10, 2022 9:21:40 PM
> To: Artur Hermano <artur.hermano_at_hotmail.com>
> Cc: KS UIUC <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: hmassrepart
>
> Hi Artur,
> When you invoke psfgen, it will report the version number in the tkcon
> and/or VMD console.
> I'm sure it is in the release notes, but I've just looked and cannot find
> the specific release notes.
> I don't use hmassrepart myself, but I would expect people are using
> 1.9.4aXX.
> Best
> Mike
>
> On Feb 10, 2022, at 3:32 PM, Artur Hermano
> <[1]artur.hermano_at_hotmail.com> wrote:
> Hello Mike,
> I am not sure what the version of my psfgen is, but should I assume that
> everyone who's been using hmassrepart in NAMD is actually using VMD
> latest release 1.9.4?
> Best,
> Artur
>
> --------------------------------------------------------------------------
>
> From: CHARLES MCCALLUM <[2]cmccallum_at_me.com>
> Sent: Thursday, February 10, 2022 20:03
> To: Artur Hermano <[3]artur.hermano_at_hotmail.com>
> Cc: KS UIUC <[4]vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: hmassrepart
>
> Hi Artur,
> What is the psfgen version? I believe it has to be at least 2.0.
> 1.9.3 is the current released version of VMD, but the alphas are at
> 1.9.4a50 or so, with psfgen 2.0.
> Best
> Mike
>
> On Feb 10, 2022, at 2:05 PM, Artur Hermano
> <[5]artur.hermano_at_hotmail.com> wrote:
> Hello VMD community!
> I want to generate a psf file with hydrogen mass repartitioning, but
> the command for it appears to be invalid...
> I've tried through TkConsole:
> >package require psfgen
> >resetpsf
> >readpsf my.psf
> >hmassrepart
> >writepsf my.heavy.psf
> But I receive an invalid command name "hmassrepart" message and it
> doesn't work. I have also tried including the hmassrepart command in
> an input file directly to the psfgen binary, but have received the
> same error. My VMD version is 1.9.3, so I don't really know what is
> going on with this error.
> Can anybody help me out?
> Any help is very much appreciated!
> Thanks!
> Artur
>
> --
> Mike McCallum
> Morada/Stockton CA, USA
> cmccallum at me ^dot^ com
>
> --
> Mike McCallum
> Morada/Stockton CA, USA
> cmccallum at me ^dot^ com
>
> References
>
> Visible links
> 1. mailto:artur.hermano_at_hotmail.com
> 2. mailto:cmccallum_at_me.com
> 3. mailto:artur.hermano_at_hotmail.com
> 4. mailto:vmd-l_at_ks.uiuc.edu
> 5. mailto:artur.hermano_at_hotmail.com 

--
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/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/