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 <[email protected]> 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
[email protected] | (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
[email protected] | (540) 231-3129
http://www.thelemkullab.com
==================================================
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