co-factor FAD in autodock-vina
Dear Chimera Design Team, We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
Dear Ching Song, I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8. I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0. Then I opened some other small molecule structure to use as ligand, #1. Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully. I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 8, 2014, at 8:27 PM, 宋青 <chingsong962005@sas.ustb.edu.cn> wrote:
Dear Chimera Design Team,
We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help.
-- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
We will try it again. Thanks a lot! Ching
-----原始邮件----- 发件人: "Elaine Meng" <meng@cgl.ucsf.edu> 发送时间: 2014-10-10 02:41:12 (星期五) 收件人: "宋青" <chingsong962005@sas.ustb.edu.cn> 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] co-factor FAD in autodock-vina
Dear Ching Song, I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8.
I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0.
Then I opened some other small molecule structure to use as ligand, #1.
Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully.
I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2014, at 8:27 PM, 宋青 <chingsong962005@sas.ustb.edu.cn> wrote:
Dear Chimera Design Team,
We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help.
-- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
Dear Elaine, Thank you for your help! I was able to dock a sugar with the FAD in situ, but only under following conditions: (1) change names of hydrogen atoms of the hydroxy groups of FAD from HOx to HxO; (2) for dockprep, calculate charges of FAD using method of Gasteiger instead of AM1-BCC. Hope the information is useful as user feedback. Best regards, Ching -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
-----原始邮件----- 发件人: "Elaine Meng" <meng@cgl.ucsf.edu> 发送时间: 2014-10-10 02:41:12 (星期五) 收件人: "宋青" <chingsong962005@sas.ustb.edu.cn> 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] co-factor FAD in autodock-vina
Dear Ching Song, I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8.
I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0.
Then I opened some other small molecule structure to use as ligand, #1.
Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully.
I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2014, at 8:27 PM, 宋青 <chingsong962005@sas.ustb.edu.cn> wrote:
Dear Chimera Design Team,
We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help.
-- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
Dear Ching, Thanks for the information — sorry that you found problems!
From your description, it sounds like the Vina prep scripts don’t like the Chimera-generated hydrogen names for the nonstandard residue (FAD). When I tested with FAD after your first question, I didn’t add hydrogens in Chimera, and in our earlier tests of Vina with Chimera hydrogen addition, we hadn’t tried structures with FAD.
I’m not sure what exactly was the problem with AM1-BCC, but we have noticed before that this method can have problems with residues with highly charged parts like the phosphates of FAD. Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 10, 2014, at 11:41 PM, 宋青 <chingsong962005@sas.ustb.edu.cn> wrote:
Dear Elaine,
Thank you for your help! I was able to dock a sugar with the FAD in situ, but only under following conditions: (1) change names of hydrogen atoms of the hydroxy groups of FAD from HOx to HxO; (2) for dockprep, calculate charges of FAD using method of Gasteiger instead of AM1-BCC. Hope the information is useful as user feedback. Best regards, Ching -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
-----原始邮件----- 发件人: "Elaine Meng" <meng@cgl.ucsf.edu> 发送时间: 2014-10-10 02:41:12 (星期五) 收件人: "宋青" <chingsong962005@sas.ustb.edu.cn> 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] co-factor FAD in autodock-vina
Dear Ching Song, I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8.
I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0.
Then I opened some other small molecule structure to use as ligand, #1.
Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully.
I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2014, at 8:27 PM, 宋青 <chingsong962005@sas.ustb.edu.cn> wrote:
Dear Chimera Design Team,
We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help.
-- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks for your continuous support! We will keep you posted of our Chimera experience! Ching
-----原始邮件----- 发件人: "Elaine Meng" <meng@cgl.ucsf.edu> 发送时间: 2014-10-14 08:51:13 (星期二) 收件人: "宋青" <chingsong962005@sas.ustb.edu.cn> 抄送: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> 主题: Re: [Chimera-users] co-factor FAD in autodock-vina
Dear Ching, Thanks for the information — sorry that you found problems!
From your description, it sounds like the Vina prep scripts don’t like the Chimera-generated hydrogen names for the nonstandard residue (FAD). When I tested with FAD after your first question, I didn’t add hydrogens in Chimera, and in our earlier tests of Vina with Chimera hydrogen addition, we hadn’t tried structures with FAD.
I’m not sure what exactly was the problem with AM1-BCC, but we have noticed before that this method can have problems with residues with highly charged parts like the phosphates of FAD.
Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 10, 2014, at 11:41 PM, 宋青 <chingsong962005@sas.ustb.edu.cn> wrote:
Dear Elaine,
Thank you for your help! I was able to dock a sugar with the FAD in situ, but only under following conditions: (1) change names of hydrogen atoms of the hydroxy groups of FAD from HOx to HxO; (2) for dockprep, calculate charges of FAD using method of Gasteiger instead of AM1-BCC. Hope the information is useful as user feedback. Best regards, Ching -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
-----原始邮件----- 发件人: "Elaine Meng" <meng@cgl.ucsf.edu> 发送时间: 2014-10-10 02:41:12 (星期五) 收件人: "宋青" <chingsong962005@sas.ustb.edu.cn> 抄送: chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] co-factor FAD in autodock-vina
Dear Ching Song, I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8.
I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0.
Then I opened some other small molecule structure to use as ligand, #1.
Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully.
I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2014, at 8:27 PM, 宋青 <chingsong962005@sas.ustb.edu.cn> wrote:
Dear Chimera Design Team,
We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help.
-- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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宋青