VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue May 22 2018 - 13:40:54 CDT

Hi Fan,

Fragments are never specified by the user. Instead, VMD builds up a fragment based on connected atoms who share the same chain and segname. Since your chain identifiers aren't correct, what I'd do is set the chain and segname to something arbitrary and uniform, and ask for VMD to reanalyze your system, so that it will only consider bonding when determining fragments. So something like:

set asel [atomselect top "all"]
$asel set chain X
$asel set segname SGN
mol reanalyze top

Note that since ions are typically *not* connected to anything, each individual ion will always be its own fragment.

-Josh

On 2018-05-22 11:46:24-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Hi every one
I downloaded a psf and a pdb file online. But the fragments are completely wrong because it is not biological system, also the chain is not right,but the connection and atom type are correct. So I wander how can delete the default fragments and redefine fragments in vmd?

The system has two layers and ion between them so I want to define the first layer as fragment 1 and second layer as fragment 2 and define ions as fragment 3.

Can I do that in VMD?

Fan