sybyl vs amber atom types in ChimeraX
Dear ChimeraX community, I hope this message finds you well. I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein. Chimera does not manage to parametrize my protein at all, which is why I switched to ChimeraX. ChimeraX does manage to generate a mol2 file, but it writes sybyl atom types. Despite looking on forums, I have not found a feature like in Chimera to write amber atom types instead. I was wondering if such a feature exists in ChimeraX ? Thanks in advance, Best, Laurène Jacquot PSL University, ChimieParisTech
On Fri, Mar 14, 2025, laurene.jacquot via ChimeraX-users wrote:
I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein.
I don't have a ChimeraX answer here, but rather a question: why do you need a protein mol2 file with Amber atom types? Amber workflows would not create a mol2 file for an entire protein; but of course, you may need such a file for some other purpose. If so, we may be able to find some Amber tools that does this (or avoids needing it), if the ChimeraX folks themselves don't have a solution. ....dave case
Hi Laurene, Like Dave, I am somewhat curious why you need you would need Amber types for an entire protein. Nonetheless, you can write such a file by adding “gaffType true” to the command you are using to save the Mol2 file (after running addcharge on the structure, which adds the GAFF types). --Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 14, 2025, at 8:08 AM, David A Case via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
On Fri, Mar 14, 2025, laurene.jacquot via ChimeraX-users wrote:
I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein.
I don't have a ChimeraX answer here, but rather a question: why do you need a protein mol2 file with Amber atom types? Amber workflows would not create a mol2 file for an entire protein; but of course, you may need such a file for some other purpose. If so, we may be able to find some Amber tools that does this (or avoids needing it), if the ChimeraX folks themselves don't have a solution.
....dave case
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Here's the help for the "save" command Mol2 options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mol2> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 17, 2025, at 2:00 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Laurene, Like Dave, I am somewhat curious why you need you would need Amber types for an entire protein. Nonetheless, you can write such a file by adding “gaffType true” to the command you are using to save the Mol2 file (after running addcharge on the structure, which adds the GAFF types).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 14, 2025, at 8:08 AM, David A Case via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
On Fri, Mar 14, 2025, laurene.jacquot via ChimeraX-users wrote:
I am a master student currently working on a project where I need to generate a mol2 file with amber atom types for a protein.
I don't have a ChimeraX answer here, but rather a question: why do you need a protein mol2 file with Amber atom types? Amber workflows would not create a mol2 file for an entire protein; but of course, you may need such a file for some other purpose. If so, we may be able to find some Amber tools that does this (or avoids needing it), if the ChimeraX folks themselves don't have a solution.
....dave case
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
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David A Case -
Elaine Meng -
Eric Pettersen -
laurene.jacquot