[gmx-users] select an atom for "only" residue with make_ndx

[Justin Lemkul]

On 5/16/19 5:44 AM, ABEL Stephane wrote:
> Thanks Justin
>
> but it does not work either
>
> LIPIDC is indeed in a group (#27)
>
> So I when typed with GMX5.1.4 or GMX2018.2
>
> LIPIDC & a C31 | a C32 | a C33  ---> Syntax error: "LIPIDC & a C31 | a C32 | a C33"
> 27 & a C31 | a C32 | a C33  ---> the command works  but I selected "all" the C31, C32 and C33 atoms and not only those in the LIPIDC group

Sorry, the correct syntax is:

27 & a C31 C32 C33

-Justin

> Stéphane
>
> On 5/15/19 11:03 AM, ABEL Stephane wrote:
>> Hello all,
>>
>> I am currently doing simulations of a model of membranes with different types of lipids (LIPIDA, LIPIDB and LIPIDC)  and I would like to select a group of  atoms for only the same lipid with make_ndx. Below an example
>>
>> Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with the same name (C31, C32 and C33). With make_ndx I would like to have the atoms C33 and C32 for "only" the LIPIDC
>>
>> So If I do
>>
>> rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 lipid types.
>> So what is the exact command
> Each different [moleculetype] already has its own default group, so
> choosing atoms in LIPIDC should be as simple as:
>
> N & a C31 | a C32 | a C33
>
> where N is the group corresponding to LIPIDC.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================