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

[ABEL Stephane]

Thanks Justin it worked. 

For the record, I have also found that 

27 & a C31 C32 C33 is equivalent to a C31 | aC32 | aC33  &  rLIPIDC or aC31 | aC32 | aC33  &  27. 

Note For the two latter commands  the order of "r27 or rLIPIDC" is important

Thanks again 

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

> St?phane
>
> 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

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



------------------------------

Message: 5
Date: Thu, 16 May 2019 13:55:33 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Charmm 36m
Message-ID: <5a0fe974-b580-dff7-74a3-98ccd6365d0d at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 5/15/19 3:54 PM, Coire Gavin-Hanner wrote:
> Dear Gromacs users,
>
> I am trying to use the charmm36m forcefield to simulate a protein. The most recent release of charmm36 includes 36m and the ability to toggle between the two. Is 36m the default state?

Yes, though it is possible to use the old C36 parameters with the
(hopefully very clear) define statement:

define = -DUSE_OLD_C36

Otherwise, the parameters used are C36m.

-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

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



------------------------------

Message: 6
Date: Thu, 16 May 2019 18:13:34 +0000 (UTC)
From: mary ko <maryko2019 at yahoo.com>
To: Discussion List for GROMACS Users
        <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] number of coordinates in coordinate file does not
        match   topology
Message-ID: <172035957.1411431.1558030414662 at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8

Hello all
I want to run a simulation of a protein from PDB data bank with a ligand. It has two chains and I need only chain A. when I delete chain B in CHIMERA and try to run the simulation, it stops at the gmx_mpi grompp -f ions.mdp -c solve.pdb -p topol.top -o ions.tpr step with the error of number of coordinates in the solve.pdb (143982) does not match the topol.top (143983). I checked the .pdb file and it starts from residue 13. Do I get the error because of that residues not being sorted from 1, since I use the same method for the sorted files and they run without errors.Thank you

------------------------------

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