VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 16 2010 - 22:21:50 CDT

On Mon, Aug 16, 2010 at 9:29 PM, Gregorio Alanislobato
<gregorio.alanislobato_at_kaust.edu.sa> wrote:
> Hi everyone,
>
> I've got two coarse grained proteins with 130 atoms each and no matter what
> selection I type in the RMSD calculator, I obtain the message "Selection
> contains no atoms. RMSD calculation not possible". What can be wrong?

your input. please read the documentation about atom selections
in the VMD user's guide again. keep in mind that most of the
heuristics that the selection language users, require pdb style
naming conventions, which are usually not given for any
coarse grain model. VMD doesn't know what your input
really stands for. it is only a computer program.

axel.

>
> Thanks again.
>
> Regards,
> --
> Gregorio Alanís Lobato, BSc
> 4700 KAUST Mail Box: 1899
> Thuwal 23955–6900, KSA
> Student ID: 100037943
> Badge #: 101969
> Mobile Phone: +966-564-75-14-14
> e-mail: gregorio.alanislobato_at_kaust.edu.sa
>
>
>
> On 16 August 2010 14:58, Mert Gür <gurmert_at_gmail.com> wrote:
>>
>> Dear Gregorio,
>> Type "name CA" instead of "protein" in the RMSD plugin
>> Best,
>> Mert
>>
>> On Mon, Aug 16, 2010 at 8:13 PM, Gregorio Alanislobato
>> <gregorio.alanislobato_at_kaust.edu.sa> wrote:
>> > Hi,
>> >
>> > I would like to measure the RSMD between two coarse grained molecules
>> > but
>> > VMD keeps saying it is not possible. Do anyone know of a way to do this?
>> >
>> > Thanks in advance.
>> >
>> > Regards,
>> > --
>> > Gregorio Alanís Lobato, BSc
>> > 4700 KAUST Mail Box: 1899
>> > Thuwal 23955–6900, KSA
>> > Student ID: 100037943
>> > Badge #: 101969
>> > Mobile Phone: +966-564-75-14-14
>> > e-mail: gregorio.alanislobato_at_kaust.edu.sa
>> >
>
>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.