VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 23 2011 - 09:30:52 CDT

On Tue, Aug 23, 2011 at 6:49 AM, Moeed <lecielll_at_googlemail.com> wrote:
> Hi John,
>
> Thanks. Yes, I am using gro. file which uses nanometers. This means every
> time I have to change the units?

no. all plugins for gromacs based file formats transparently
convert between nanometers and angstroms.

please provide an example showing what exactly
your problem is.

axel.

> On Mon, Aug 15, 2011 at 12:21 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>> Hi,
>>  This is usually caused by problems with the interpretation of the
>> coordinate units in the files being loaded.  Is it possible that you've
>> got your atomic coordinates in units of nanometers, but have saved them
>> to a file format (e.g. PDB) that expects Angstroms?
>>
>> Cheers,
>>  John Stone
>>  vmd_at_ks.uiuc.edu
>>
>> On Mon, Aug 15, 2011 at 12:09:51PM -0400, Moeed wrote:
>> >    Hello all,
>> >
>> >    I have a problem visualizing my structure in vmd. Once I load
>> > structure
>> >    and trajectory files file I see some artificial bonds connecting all
>> > atoms
>> >    while there is no bond between them. Has anyone any ideas why this is
>> >    happening?
>> >
>> >    Thank you,
>>
>> --
>> NIH Resource 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/       Fax: 217-244-6078
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.