From: amin sagar (
Date: Mon Oct 29 2018 - 05:27:38 CDT

I think the gro file doesn't store the chain information. There is probably
a way to add that information in the converted pdb file using trjconv.

Another way would be to use index. You can find the atom numbers of the
residues you want to select by opening the gro file in a text editor and
then selecting as, for example

index 1 to 150

Within VMD, if you make a selection in the tk console like

set sel [atomselect top "protein and resid 1 to 50"]

and then get the index by

$sel get index

you should see two discontinuous series of numbers like 10,11,12, ......
100 and 150,151,152.....250.

One of these stretch should be your required selection.

You can then try both using the index, for example,

index 10 to 100

and one of the two should be what you want.

There are probably simpler methods out there.


On Mon, Oct 29, 2018 at 9:48 AM Raag Saluja <> wrote:

> You’re right. Your command (resid 1 to 50 and protein and chain A) works
> perfect with the pdb file downloaded from protein data bank. However, I was
> trying to do the same with a pdb file obtained after simulating the protein
> (I simulated it using gromacs and converted the final gro file into pdb),
> but in vain. How do you suggest I go about this, please?
> On Mon, 29 Oct 2018 at 1:24 PM, amin sagar <> wrote:
>> Just to check, are you sure your chain name is A? Otherwise it should be
>> replaced with the name of the chain you would like to select.
>> On Mon, 29 Oct 2018 at 8:51 AM, Raag Saluja <>
>> wrote:
>>> Thank you for your prompt replies! I tried both resid 1 to 50 and chain
>>> A; and resid 1 to 50 and protein and chain A. Neither worked! The selected
>>> area just got deselected.
>>> On Mon, 29 Oct 2018 at 1:17 PM, amin sagar <>
>>> wrote:
>>>> Hi. Something like
>>>> protein and chain A and resid 1 to 50
>>>> should work.
>>>> Amin.
>>>> On Mon, 29 Oct 2018 at 8:38 AM, Raag Saluja <>
>>>> wrote:
>>>>> Hi!
>>>>> I am working on a heterodimer. I wanted to highlight certain residues
>>>>> and keep the rest of the protein translucent. So I did create rep and then
>>>>> selected the residues by giving the command "(resid 1 to 50) and
>>>>> (protein)".
>>>>> However, this selects the first 50 residues in both the chains. What
>>>>> do I do so that only the first 50 residues are selected, be they in the
>>>>> first or the second chain
>>>>> (and not 50 each of both the chains)?
>>>>> Thank you in advance!
>>>>> Regards,
>>>>> Raag