Dear all,
In gromacs tutorial its written that pdb2gmx can be used for cofactors like NAD(H) and ATP, my question is how can i use it on my pdb file of ATP molecule. Do i need to change the residue name? Right now I'm getting the error of unknown residue type LIG.
I want to generate topology files for MD simulations using gromacs.
I have attached my ATP pdb file. Looking forward for a reply.
Thanks and Regards,
Raghav
These are the force fields that natively support ATP in GROMACS:
$ grep "ATP" *.ff/*.rtp
charmm36.ff/merged.rtp:[ ATP ]
gromos43a1.ff/aminoacids.rtp:[ ATP ]
gromos43a2.ff/aminoacids.rtp:[ ATP ]
gromos45a3.ff/aminoacids.rtp:[ ATP ]
gromos53a5.ff/aminoacids.rtp:[ ATP ]
gromos53a6.ff/aminoacids.rtp:[ ATP ]
gromos54a7.ff/aminoacids.rtp:[ ATP ]
As stated above, if you want parameters for other force fields, you will need to obtain them from another source.
The residue name needs to match that of the entry in the .rtp file. pdb2gmx has no idea what "LIG" is. If it's ATP, it needs to be named ATP.
http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database
Dear Justin Lemkul ,
I changed the ligand name from "LIG" to "ATP" in my pdb file but pdb2gmx is still showing the same error "Unknown residue type ATP". I know it means that I will have to add this residue in the .rtp file of the corresponding forcefield, but the tutorial said that pdb2gmx can be used for cofactors like NAD(H) and ATP, so i was wondering which forcefield incorporates the ATP.
Regards,
Raghav
ATP parameters are in amber format. http://research.bmh.manchester.ac.uk/bryce/amber/. Convert them into gromacs format using amb2gmx or acpype code.
And then include the itp file in the topol.top of the protein generated from pdb2gmx. Or check out charmmgui server.
These are the force fields that natively support ATP in GROMACS:
$ grep "ATP" *.ff/*.rtp
charmm36.ff/merged.rtp:[ ATP ]
gromos43a1.ff/aminoacids.rtp:[ ATP ]
gromos43a2.ff/aminoacids.rtp:[ ATP ]
gromos45a3.ff/aminoacids.rtp:[ ATP ]
gromos53a5.ff/aminoacids.rtp:[ ATP ]
gromos53a6.ff/aminoacids.rtp:[ ATP ]
gromos54a7.ff/aminoacids.rtp:[ ATP ]
As stated above, if you want parameters for other force fields, you will need to obtain them from another source.
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