Hi,
I want to do molecular Dynamic Simulations of an enzyme at three different pHs.
I have protonated my protein structure at 3 different pHs in Discovery Studio. Now I want to continue the process in Gromacs.
But it seems that gromacs does not accept the new protonation states that I have introduced to the structures.
I have used CHARMM forcefield in Discovery studio and again I am choosing CHARMM27 in gromacs.
From the first point, when I run the command for creating topology and structure files (gmx pdb2gmx -f BG-S-pH5i.pdb -o 3AHY-pH5_sep12.gro -water spce )
I am receiving this error:
Fetal error:
Atom HE2 in residue GLU 18 was not found in rtp entry GLU with 15 atoms while sorting atoms.
I saw in the manual that rtp files can be used for introducing new ionization states to residues. But I already have the correct protonations and I only want the gromacs to recognize them.
I would greatly appreciate your advice in this regards.
Thanks,
Mina
Zhaoxi Sun
Dear Zhaoxi,
Thanks for your comment.
Actually, I also tried to protonate my proteins with the PROPKA3.1 server with the option of setting the names based on CHARMM nomenclatures in the created PDB files. But then I received an error regarding this new nomenclature.
The protonated Glu residues were showing up as GLUP. But it seems that CHARMM27 still does not recognize that.
Do you have any suggestions how the protonated forms should get named?
Or is there any reference you could introduce me to see the nomenclatures for CHARMM27?
Thanks,
Mina
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 2012 Jul; 40(Web Server issue): W537–W541. doi: 10.1093/nar/gks375
Please follow this paper for protonation states of amino acids before MD simulation.
This is the link for to define protonation states using pdb structure:
http://biophysics.cs.vt.edu/
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