Circular DNA Construction and DNA Origami in Chimera 1.17.3
I am writing to inquire about the capabilities of Chimera 1.17.3 for constructing circular DNA and DNA origami, and to seek guidance on saving PDB output files for future use in GROMACS with the AMBER force field.
Firstly, I am interested in constructing circular DNA using Chimera 1.17.3. Could you please provide information or guidance on whether this version of Chimera supports circular DNA construction? If so, I would appreciate any instructions or resources that can help me achieve this.
Additionally, I would like to explore the possibility of building DNA origami structures using Chimera 1.17.3. Could you please inform me if this version of Chimera has the functionality to create DNA origami structures? If it does, any pointers or documentation on how to get started with DNA origami in Chimera would be highly valuable.
Lastly, my goal is to save the PDB output files generated in Chimera for subsequent use in GROMACS with the AMBER force field. Could you provide guidance on the best practices for saving PDB files from Chimera for compatibility with GROMACS and the AMBER force field? Any specific settings or considerations to ensure seamless integration would be greatly appreciated.
Hello, Chimera cannot directly build circular DNA. The options for DNA building are for regular (linear) double helices only. How you would do that: Menu: Tools... Structure Editing... Build Structure, and in that tool, go to the Start Structure section. There is an option for "helical DNA/RNA". However, that would just give you a linear piece of double helix from the sequence that you enter. https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
Although you could try to manually rotate some bonds to change the conformation and add a bond to connect one end to the other, I believe that this would be extremely difficult to do in Chimera and that you may need to find some other program to build the circular DNA instead. I have never tried to do this, so I don't have many ideas except for CanDo mentioned below.
I also don't have any specific advice for using an output PDB file in GROMACS. Chimera aims to write standard PDB format using standard atom names. I don't know if GROMACS has special requirements that are different than those, however. Maybe some GROMACS experts on this mailing list can advise?
See the following link for the CanDo program, which is for designing DNA nanostructures (like origami) and I see one example with circular DNA, but it writes files in a .cndo format, not PDB. Maybe it could be converted to pdb, but I have not investigated, nor have I ever used CanDo. See example 4 for the circular DNA. https://cando-dna-origami.org/atomic-model-generator/
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2023, at 4:23 AM, fatemeh F via Chimera-users chimera-users@cgl.ucsf.edu wrote:
I am writing to inquire about the capabilities of Chimera 1.17.3 for constructing circular DNA and DNA origami, and to seek guidance on saving PDB output files for future use in GROMACS with the AMBER force field.
Firstly, I am interested in constructing circular DNA using Chimera 1.17.3. Could you please provide information or guidance on whether this version of Chimera supports circular DNA construction? If so, I would appreciate any instructions or resources that can help me achieve this.
Additionally, I would like to explore the possibility of building DNA origami structures using Chimera 1.17.3. Could you please inform me if this version of Chimera has the functionality to create DNA origami structures? If it does, any pointers or documentation on how to get started with DNA origami in Chimera would be highly valuable.
Lastly, my goal is to save the PDB output files generated in Chimera for subsequent use in GROMACS with the AMBER force field. Could you provide guidance on the best practices for saving PDB files from Chimera for compatibility with GROMACS and the AMBER force field? Any specific settings or considerations to ensure seamless integration would be greatly appreciated.
Dear Elaine I wanted to convey my sincere appreciation for your previous clarifications and valuable suggestions.
I have encountered another question in my research, and I was hoping you could provide some guidance. Specifically, I am exploring the feasibility of creating DNA origami structures using alternative software tools. Afterward, I would like to manipulate these structures by adding or removing bonds and making adjustments using Chimera. If this is possible, could you please explain the steps involved?
My inquiry stems from the challenges I have encountered while attempting to construct even simple DNA structures using other software or server like the 3xDNA web server. To elaborate, I faced an issue with the "pdb2gmx" module in GROMACS, which reported that "atom P in residue DG1 was not found in rtp entry DG5." It seems that "pdb2gmx" does not support phosphorylated terminals in DNA. Interestingly, when I constructed straight DNA with Chimera and saved it as a PDB file in Amber format, I did not encounter this problem.
I would greatly appreciate any insights or recommendations you might have regarding alternative software solutions or approaches that would enable me to achieve my goal of creating and manipulating DNA origami structures and subsequently converting them into a PDB format compatible with AMBER.
Once again, I extend my gratitude for your assistance.
Best regards, Fatemeh
On Fri, Sep 29, 2023 at 4:27 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hello, Chimera cannot directly build circular DNA. The options for DNA building are for regular (linear) double helices only. How you would do that: Menu: Tools... Structure Editing... Build Structure, and in that tool, go to the Start Structure section. There is an option for "helical DNA/RNA". However, that would just give you a linear piece of double helix from the sequence that you enter. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...
Although you could try to manually rotate some bonds to change the conformation and add a bond to connect one end to the other, I believe that this would be extremely difficult to do in Chimera and that you may need to find some other program to build the circular DNA instead. I have never tried to do this, so I don't have many ideas except for CanDo mentioned below.
I also don't have any specific advice for using an output PDB file in GROMACS. Chimera aims to write standard PDB format using standard atom names. I don't know if GROMACS has special requirements that are different than those, however. Maybe some GROMACS experts on this mailing list can advise?
See the following link for the CanDo program, which is for designing DNA nanostructures (like origami) and I see one example with circular DNA, but it writes files in a .cndo format, not PDB. Maybe it could be converted to pdb, but I have not investigated, nor have I ever used CanDo. See example 4 for the circular DNA. https://cando-dna-origami.org/atomic-model-generator/
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2023, at 4:23 AM, fatemeh F via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
I am writing to inquire about the capabilities of Chimera 1.17.3 for
constructing circular DNA and DNA origami, and to seek guidance on saving PDB output files for future use in GROMACS with the AMBER force field.
Firstly, I am interested in constructing circular DNA using Chimera
1.17.3. Could you please provide information or guidance on whether this version of Chimera supports circular DNA construction? If so, I would appreciate any instructions or resources that can help me achieve this.
Additionally, I would like to explore the possibility of building DNA
origami structures using Chimera 1.17.3. Could you please inform me if this version of Chimera has the functionality to create DNA origami structures? If it does, any pointers or documentation on how to get started with DNA origami in Chimera would be highly valuable.
Lastly, my goal is to save the PDB output files generated in Chimera for
subsequent use in GROMACS with the AMBER force field. Could you provide guidance on the best practices for saving PDB files from Chimera for compatibility with GROMACS and the AMBER force field? Any specific settings or considerations to ensure seamless integration would be greatly appreciated.
Dear Fatemah, I don't know much about DNA origami, so I didn't have ideas about alternative software solutions. The CanDo program mentioned in the previous message was the only idea I had.
As for how to make further changes in Chimera, see the following help links for details...
How to rotate bonds:
- Build Structure tool (menu: tools.. Structure Editing... Build Structure), the Adjust Torsions section https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
- there is also a "rotation" command but it is not as convenient as the above https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html
How to add or remove bonds:
- Build Structure tool, the Adjust Bonds section https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
- or use "bond" command https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2023, at 5:58 AM, fatemeh F fadaeifatemeh1@gmail.com wrote:
Dear Elaine I wanted to convey my sincere appreciation for your previous clarifications and valuable suggestions.
I have encountered another question in my research, and I was hoping you could provide some guidance. Specifically, I am exploring the feasibility of creating DNA origami structures using alternative software tools. Afterward, I would like to manipulate these structures by adding or removing bonds and making adjustments using Chimera. If this is possible, could you please explain the steps involved?
My inquiry stems from the challenges I have encountered while attempting to construct even simple DNA structures using other software or server like the 3xDNA web server. To elaborate, I faced an issue with the "pdb2gmx" module in GROMACS, which reported that "atom P in residue DG1 was not found in rtp entry DG5." It seems that "pdb2gmx" does not support phosphorylated terminals in DNA. Interestingly, when I constructed straight DNA with Chimera and saved it as a PDB file in Amber format, I did not encounter this problem.
I would greatly appreciate any insights or recommendations you might have regarding alternative software solutions or approaches that would enable me to achieve my goal of creating and manipulating DNA origami structures and subsequently converting them into a PDB format compatible with AMBER.
Once again, I extend my gratitude for your assistance.
Best regards, Fatemeh
On Fri, Sep 29, 2023 at 4:27 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hello, Chimera cannot directly build circular DNA. The options for DNA building are for regular (linear) double helices only. How you would do that: Menu: Tools... Structure Editing... Build Structure, and in that tool, go to the Start Structure section. There is an option for "helical DNA/RNA". However, that would just give you a linear piece of double helix from the sequence that you enter. https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
Although you could try to manually rotate some bonds to change the conformation and add a bond to connect one end to the other, I believe that this would be extremely difficult to do in Chimera and that you may need to find some other program to build the circular DNA instead. I have never tried to do this, so I don't have many ideas except for CanDo mentioned below.
I also don't have any specific advice for using an output PDB file in GROMACS. Chimera aims to write standard PDB format using standard atom names. I don't know if GROMACS has special requirements that are different than those, however. Maybe some GROMACS experts on this mailing list can advise?
See the following link for the CanDo program, which is for designing DNA nanostructures (like origami) and I see one example with circular DNA, but it writes files in a .cndo format, not PDB. Maybe it could be converted to pdb, but I have not investigated, nor have I ever used CanDo. See example 4 for the circular DNA. https://cando-dna-origami.org/atomic-model-generator/
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2023, at 4:23 AM, fatemeh F via Chimera-users chimera-users@cgl.ucsf.edu wrote:
I am writing to inquire about the capabilities of Chimera 1.17.3 for constructing circular DNA and DNA origami, and to seek guidance on saving PDB output files for future use in GROMACS with the AMBER force field.
Firstly, I am interested in constructing circular DNA using Chimera 1.17.3. Could you please provide information or guidance on whether this version of Chimera supports circular DNA construction? If so, I would appreciate any instructions or resources that can help me achieve this.
Additionally, I would like to explore the possibility of building DNA origami structures using Chimera 1.17.3. Could you please inform me if this version of Chimera has the functionality to create DNA origami structures? If it does, any pointers or documentation on how to get started with DNA origami in Chimera would be highly valuable.
Lastly, my goal is to save the PDB output files generated in Chimera for subsequent use in GROMACS with the AMBER force field. Could you provide guidance on the best practices for saving PDB files from Chimera for compatibility with GROMACS and the AMBER force field? Any specific settings or considerations to ensure seamless integration would be greatly appreciated.
Thank you very much for your feedback. Best Regards, Fatemeh,
On Fri, Sep 29, 2023 at 7:17 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Fatemah, I don't know much about DNA origami, so I didn't have ideas about alternative software solutions. The CanDo program mentioned in the previous message was the only idea I had.
As for how to make further changes in Chimera, see the following help links for details...
How to rotate bonds:
- Build Structure tool (menu: tools.. Structure Editing... Build
Structure), the Adjust Torsions section < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...
- there is also a "rotation" command but it is not as convenient as the
above https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html
How to add or remove bonds:
- Build Structure tool, the Adjust Bonds section
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...
- or use "bond" command
https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 29, 2023, at 5:58 AM, fatemeh F fadaeifatemeh1@gmail.com wrote:
Dear Elaine I wanted to convey my sincere appreciation for your previous
clarifications and valuable suggestions.
I have encountered another question in my research, and I was hoping you
could provide some guidance. Specifically, I am exploring the feasibility of creating DNA origami structures using alternative software tools. Afterward, I would like to manipulate these structures by adding or removing bonds and making adjustments using Chimera. If this is possible, could you please explain the steps involved?
My inquiry stems from the challenges I have encountered while attempting
to construct even simple DNA structures using other software or server like the 3xDNA web server. To elaborate, I faced an issue with the "pdb2gmx" module in GROMACS, which reported that "atom P in residue DG1 was not found in rtp entry DG5." It seems that "pdb2gmx" does not support phosphorylated terminals in DNA. Interestingly, when I constructed straight DNA with Chimera and saved it as a PDB file in Amber format, I did not encounter this problem.
I would greatly appreciate any insights or recommendations you might
have regarding alternative software solutions or approaches that would enable me to achieve my goal of creating and manipulating DNA origami structures and subsequently converting them into a PDB format compatible with AMBER.
Once again, I extend my gratitude for your assistance.
Best regards, Fatemeh
On Fri, Sep 29, 2023 at 4:27 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hello, Chimera cannot directly build circular DNA. The options for DNA
building are for regular (linear) double helices only. How you would do that: Menu: Tools... Structure Editing... Build Structure, and in that tool, go to the Start Structure section. There is an option for "helical DNA/RNA". However, that would just give you a linear piece of double helix from the sequence that you enter.
<
https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...
Although you could try to manually rotate some bonds to change the
conformation and add a bond to connect one end to the other, I believe that this would be extremely difficult to do in Chimera and that you may need to find some other program to build the circular DNA instead. I have never tried to do this, so I don't have many ideas except for CanDo mentioned below.
I also don't have any specific advice for using an output PDB file in
GROMACS. Chimera aims to write standard PDB format using standard atom names. I don't know if GROMACS has special requirements that are different than those, however. Maybe some GROMACS experts on this mailing list can advise?
See the following link for the CanDo program, which is for designing DNA
nanostructures (like origami) and I see one example with circular DNA, but it writes files in a .cndo format, not PDB. Maybe it could be converted to pdb, but I have not investigated, nor have I ever used CanDo. See example 4 for the circular DNA.
https://cando-dna-origami.org/atomic-model-generator/
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2023, at 4:23 AM, fatemeh F via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
I am writing to inquire about the capabilities of Chimera 1.17.3 for
constructing circular DNA and DNA origami, and to seek guidance on saving PDB output files for future use in GROMACS with the AMBER force field.
Firstly, I am interested in constructing circular DNA using Chimera
1.17.3. Could you please provide information or guidance on whether this version of Chimera supports circular DNA construction? If so, I would appreciate any instructions or resources that can help me achieve this.
Additionally, I would like to explore the possibility of building DNA
origami structures using Chimera 1.17.3. Could you please inform me if this version of Chimera has the functionality to create DNA origami structures? If it does, any pointers or documentation on how to get started with DNA origami in Chimera would be highly valuable.
Lastly, my goal is to save the PDB output files generated in Chimera
for subsequent use in GROMACS with the AMBER force field. Could you provide guidance on the best practices for saving PDB files from Chimera for compatibility with GROMACS and the AMBER force field? Any specific settings or considerations to ensure seamless integration would be greatly appreciated.
participants (2)
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Elaine Meng -
fatemeh F