VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Jun 07 2014 - 05:36:12 CDT

On Sat, Jun 7, 2014 at 5:47 AM, sunyeping <sunyeping_at_aliyun.com> wrote:

> Dear all,
>
> I wish to analyze a groamcas xtc trajectory with VMD. I load the gro
> structure file and the xtc trajectory file into VMD. The protein has three
> chains, so VMD can not prpperly recognize the atom selection. For example,
> I try to select residue 30 on chain A, but "resid 30" will select residue
> 30 in all the thains that have more than 30 reredues. So it is impossible
> to make the analysis in VMD. If the gro file is transformed into a psf
> file, can the problem be solved? but how? And is there any other solution?
> Thank you very much.
>

​VMD will do what you ask it to do with the information you provide. if you
ask for a selection of "resid 30" you get all atoms that have a residue id
of 30 which is what you observe. nothing more, nothing less and exactly
what you requested. now, if you want only a subset of those, you need to
restrict the selection more. how to do this is explained in the user's
guide. what properties are available for this, depends on the information
provided in the files that you read in. so it is up to you how​ to solve
this.

axel.

>
> Yeping Sun
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.