[gmx-users] Coarse-grained Protein-ligand simulations

[Justin Lemkul]

On 3/29/19 9:17 AM, Mac Kevin Braza wrote:
> Thank you Professor Lemkul,
>
> But would you suggest on how can I coarse-grained the ligand I am using? I
> have been searching resources online but they do not work in our part.

I don't work with CG simulations, so I'm not much help. I would think 
that a CG parametrization of a ligand would remove all the detail you'd 
normally want to see in terms of ligand-protein interactions.

-Justin

> I hope you can help us. Thank you Prof. Lemkul!
>
> Best regards,
> Mac Kevin E. Braza
>
> On Fri, Mar 29, 2019, 8:59 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 3/29/19 3:32 AM, Mac Kevin Braza wrote:
>>> Hello everyone,
>>>
>>> I am simulating a coarse-grained model of a membrane protein (GPCR) in
>>> lipid bilayer and an all-atom ligand octopamine. I build the protein,
>>> solutes, and membrane in the web server CHARMM-GUI. While, I added the
>>> ligand to the protein complex manually using the same coordinates of the
>>> coarse-grained protein model.
>>>
>>> I used the GROMACS input files from the output of CHARMM-GUI to simulate
>>> the system. I include the LIGAND.ITP (from the PRODRG Server) to the
>>> system.top and added the atom indexes in the index.ndx file.
>> Don't do this. An atomistic representation of a ligand and a CG
>> representation of everything else is incompatible. Mixing and matching
>> force fields is never a good idea. Moreover, PRODRG produces topologies
>> that are known to be unsuitable for MD simulations.
>>
>>> However, when I proceed with the second part of equilibration, the
>>> following errors occurred.
>>>
>>> *Command line*:
>>>     gmx grompp -f step6.2_equilibration.mdp -o step6.2_equilibration.tpr
>> -c
>>> step6.1_equilibration.gro -p system.top -n index.ndx
>>>
>>> Setting the LD random seed to 1722366284
>>> Generated 2391 of the 4656 non-bonded parameter combinations
>>> Excluding 1 bonded neighbours molecule type 'PROA_P'
>>> Excluding 1 bonded neighbours molecule type 'POPC'
>>> Excluding 1 bonded neighbours molecule type 'W'
>>> Excluding 1 bonded neighbours molecule type 'NA'
>>> Excluding 1 bonded neighbours molecule type 'CL'
>>> Excluding 3 bonded neighbours molecule type 'LIG'
>>> Velocities were taken from a Maxwell distribution at 303.15 K
>>> Removing all charge groups because cutoff-scheme=Verlet
>>>
>>> -------------------------------------------------------
>>> Program gmx grompp, VERSION 5.1.4
>>> Source code file: /home/gromacs-5.1.4/src/gromacs/gmxpreprocess/readir.c,
>>> line: 2690
>>>
>>> Fatal error:
>>> 20 atoms are not part of any of the T-Coupling groups
>>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>>
>>> The 20 atoms described the ligand I placed inside the protein-membrane
>>> complex. I want to know if where can this error originate and how can we
>>> fix them?
>> This simply means you haven't specified the ligand anywhere in tc-grps.
>> But again, back up and reevaluate your approach, which is far more
>> problematic than this simple index group issue.
>>
>> -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
>>
>> ==================================================
>>
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-- 
==================================================

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

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