VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Tue Oct 04 2005 - 14:03:46 CDT

Hi guys,

I have a CE atom in a methionine residue that is a little distant from its
corresponding sulfur. When I open the molecule using VMD, make some minor
rotations and then save the protein, the saved protein is missing this atom.
Presumably it was too far away to be recognized as part of the MET residue
(in fact no bond is displayed in the viewer) and was truncated. I'd rather
not have this truncated (I'll do an energy minimization later, hopefully fix
the problem that way). Can anyone tell me how to instruct VMD to not remove
atoms?

Many thanks

Sam

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
mashaojie163
Sent: Monday, October 03, 2005 9:16 PM
To: vmd; John Stone
Subject: Re: vmd-l: How can I compile win32-vmd

    Thank you
     Maybe you just provide the current windows vmd for me. I have
compiled plugins successfully by use of cygwin and was compiling vmd by use
of MSVC and now meeting some errors. Please send me the new vmd in windows .
I will compile it when I have spare time.
      Best Regards
 
Ma shaojie

   
----- Original Message -----
From: "John Stone" <johns_at_ks.uiuc.edu>
To: "mashaojie163" <mashao_jie_at_163.com>
Cc: "vmd" <vmd-l_at_ks.uiuc.edu>
Sent: Tuesday, October 04, 2005 12:15 AM
Subject: Re: vmd-l: How can I compile win32-vmd

>
> Hi,
> If you need a current build of VMD on Windows, I can provide one for
you.
> If you really want to build from source, you should be warned that the
build
> requires you to use MSVC and if you plan to build the plugins from source,

> you'll also need cygwin to get the 'make' and other utilities we're using
> there. Let me know what you're trying to do and I can help you solve
this.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Oct 02, 2005 at 01:18:11PM +0800, mashaojie163 wrote:
> >
> >
> >
> > Dear Sir:
> > I get the source code by vmd-cvs and by use of make command to
compile linux vmd. But can you tell me how I should compile window vmd. I do
not know make command in windows
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>