[gmx-users] 2 chain protein and VMD

Acoot Brett acootbrett at yahoo.com
Sun Aug 19 02:12:54 CEST 2012

Dear Rui and All,
For the initial PDB file for my MD, it contains chain A (residue 1-400) and B (residue 1-40). After I load the trajectory file to VMD, I find it has converted both chain A and B to chain X. And in chain X it contains the original sequences of both chain A and chain B, which means in Chain X it has residue 1-400 (originall from chain A) followed by residue 1-40 (originally from chain B). And if I select residue 1-40, the residue 1-40 from both the original chain A and chain B are selected. 
If I only want to highlight the X chain residue 1-40 which correspond to residue 1-40 in chain B by VMD, will you please advice a correct method?

----- Original Message -----
From: Joaquim Rui de Castro Rodrigues <joaquim.rodrigues at ipleiria.pt>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, 18 August 2012 8:43 PM
Subject: RE: [gmx-users] 2 chain protein and VMD


You could do something like this:

set sel1 [atomselect top "residue 0 to 499"]
$sel1 set chain A
set sel2 [atomselect top "residue 500 to 999"]
$sel2 set chain B

Hope this helps,
Rui Rodrigues

De: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] Em Nome De Acoot Brett [acootbrett at yahoo.com]
Enviado: sábado, 18 de Agosto de 2012 9:35
Para: Discussion list for GROMACS users
Assunto: [gmx-users] 2 chain protein and VMD

  Dear All,

After the production MD for a 2-chain protein complex (chain A and chain B) was done, I used VMD to observe the trajectory. I want to color the 2 chains in different color.

However it seems during the observation of the trajectory by VMD, VMD treated both of the 2 chains as chain X, and thus the 2 chains cannot be colored differently.

Do you have any method or suggestion to color the 2 chains in different color by VMD in the trajectory observation process?


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