Cannot Minimize the Water Molecules
Dear all, I am trying to minimize the crystal structure of a protein using Chimera. But the program could not minimize the water molecules of the protein. I added hydrogen atoms to the whole structure. But during the minimization, it is showing the following error: No MMTK name for atom "H" in standard residue "HOH" It would be very helpful for me if you can suggest what changes I should make. Thank you! Sincerely Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India
Hi Gourav, For standard residues like HOH, the atoms have to have their PDB standard names. The names for the hydrogens in water are H1 and H2, not H. The easiest way to correct these bad hydrogen names is just to delete all the hydrogens in the structure and let Chimera add them back with their correct names as a standard part of the minimization procedure. You can delete all hydrogens in your structure with the command (Favorites→Command Line) "del H". --Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 11, 2023, at 11:29 PM, Gourav Das via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all,
I am trying to minimize the crystal structure of a protein using Chimera. But the program could not minimize the water molecules of the protein. I added hydrogen atoms to the whole structure. But during the minimization, it is showing the following error: No MMTK name for atom "H" in standard residue "HOH"
It would be very helpful for me if you can suggest what changes I should make.
Thank you!
Sincerely Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India
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Thank you, Eric, for your kind help. It worked for me. Sincerely Gourav On Wed, Sep 13, 2023 at 12:12 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Gourav, For standard residues like HOH, the atoms have to have their PDB standard names. The names for the hydrogens in water are H1 and H2, not H. The easiest way to correct these bad hydrogen names is just to delete all the hydrogens in the structure and let Chimera add them back with their correct names as a standard part of the minimization procedure. You can delete all hydrogens in your structure with the command (Favorites→Command Line) "del H".
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Sep 11, 2023, at 11:29 PM, Gourav Das via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear all,
I am trying to minimize the crystal structure of a protein using Chimera. But the program could not minimize the water molecules of the protein. I added hydrogen atoms to the whole structure. But during the minimization, it is showing the following error: No MMTK name for atom "H" in standard residue "HOH"
It would be very helpful for me if you can suggest what changes I should make.
Thank you!
Sincerely Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
participants (2)
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Eric Pettersen -
Gourav Das