the version of Ambertools that are used in the command "Write prmtop"?
Dear Chimera's users, I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release? Best regards, Victor
Hi Victor, Most of Chimera uses AmberTools18 (e.g. minimization; charge addition), but specifically the tools in the Tools→Amber menu use functionality provided by sleap, which is not distributed with current versions of AmberTools. Those tools use AmberTools 1.5, which was released in 2011. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera's users,
I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release?
Best regards, Victor _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Eric, Thank you for your help. Maybe you know how to build *.prmtop file of substance namely in the GAFF force field, using Chimera's tools? Best regards, Victor вт, 26 окт. 2021 г. в 20:14, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Victor, Most of Chimera uses AmberTools18 (e.g. minimization; charge addition), but specifically the tools in the Tools→Amber menu use functionality provided by sleap, which is not distributed with current versions of AmberTools. Those tools use AmberTools 1.5, which was released in 2011.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera's users,
I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release?
Best regards, Victor _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Victor, I'm not sure I understand the question. The Write Prmtop tool will write a .prmtop file using GAFF types if necessary. That prmtop file uses a somewhat older version of the prmtop format, but most tools will still read it. --Eric
On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev@imc.macro.ru> wrote:
Dear Eric,
Thank you for your help.
Maybe you know how to build *.prmtop file of substance namely in the GAFF force field, using Chimera's tools?
Best regards, Victor
вт, 26 окт. 2021 г. в 20:14, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>>: Hi Victor, Most of Chimera uses AmberTools18 (e.g. minimization; charge addition), but specifically the tools in the Tools→Amber menu use functionality provided by sleap, which is not distributed with current versions of AmberTools. Those tools use AmberTools 1.5, which was released in 2011.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Dear Chimera's users,
I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release?
Best regards, Victor _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hello, Eric, Sorry for the delay with response. But when I chose the Tools>Amder>Write Prmtop> in the menu Select force field type I only can select 6 force fields, and GAFF could not be chosen. Could you please direct where in the Chimera menu I can select the option to build a GAFF force field using the menu "Write Prmtop"? Best regards, Victor ср, 27 окт. 2021 г. в 20:58, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Victor, I'm not sure I understand the question. The Write Prmtop tool will write a .prmtop file using GAFF types if necessary. That prmtop file uses a somewhat older version of the prmtop format, but most tools will still read it.
--Eric
On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev@imc.macro.ru> wrote:
Dear Eric,
Thank you for your help.
Maybe you know how to build *.prmtop file of substance namely in the GAFF force field, using Chimera's tools?
Best regards, Victor
вт, 26 окт. 2021 г. в 20:14, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Victor, Most of Chimera uses AmberTools18 (e.g. minimization; charge addition), but specifically the tools in the Tools→Amber menu use functionality provided by sleap, which is not distributed with current versions of AmberTools. Those tools use AmberTools 1.5, which was released in 2011.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera's users,
I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release?
Best regards, Victor _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Victor, Chimera will use GAFF types for non-standard residues in all those forcefields, and regular AMBER types for standard residues. There is no option to use GAFF types for all residues. --Eric
On Nov 8, 2021, at 10:35 AM, Victor Nazarychev <nazarychev@imc.macro.ru> wrote:
Hello, Eric,
Sorry for the delay with response. But when I chose the Tools>Amder>Write Prmtop> in the menu Select force field type I only can select 6 force fields, and GAFF could not be chosen.
Could you please direct where in the Chimera menu I can select the option to build a GAFF force field using the menu "Write Prmtop"?
Best regards, Victor
ср, 27 окт. 2021 г. в 20:58, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>>: Hi Victor, I'm not sure I understand the question. The Write Prmtop tool will write a .prmtop file using GAFF types if necessary. That prmtop file uses a somewhat older version of the prmtop format, but most tools will still read it.
--Eric
On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev@imc.macro.ru <mailto:nazarychev@imc.macro.ru>> wrote:
Dear Eric,
Thank you for your help.
Maybe you know how to build *.prmtop file of substance namely in the GAFF force field, using Chimera's tools?
Best regards, Victor
вт, 26 окт. 2021 г. в 20:14, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>>: Hi Victor, Most of Chimera uses AmberTools18 (e.g. minimization; charge addition), but specifically the tools in the Tools→Amber menu use functionality provided by sleap, which is not distributed with current versions of AmberTools. Those tools use AmberTools 1.5, which was released in 2011.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Dear Chimera's users,
I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release?
Best regards, Victor _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Eric, Thank you for your answer! Victor пн, 8 нояб. 2021 г. в 22:19, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Victor, Chimera will use GAFF types for non-standard residues in all those forcefields, and regular AMBER types for standard residues. There is no option to use GAFF types for all residues.
--Eric
On Nov 8, 2021, at 10:35 AM, Victor Nazarychev <nazarychev@imc.macro.ru> wrote:
Hello, Eric,
Sorry for the delay with response. But when I chose the Tools>Amder>Write Prmtop> in the menu Select force field type I only can select 6 force fields, and GAFF could not be chosen.
Could you please direct where in the Chimera menu I can select the option to build a GAFF force field using the menu "Write Prmtop"?
Best regards, Victor
ср, 27 окт. 2021 г. в 20:58, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Victor, I'm not sure I understand the question. The Write Prmtop tool will write a .prmtop file using GAFF types if necessary. That prmtop file uses a somewhat older version of the prmtop format, but most tools will still read it.
--Eric
On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev@imc.macro.ru> wrote:
Dear Eric,
Thank you for your help.
Maybe you know how to build *.prmtop file of substance namely in the GAFF force field, using Chimera's tools?
Best regards, Victor
вт, 26 окт. 2021 г. в 20:14, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Victor, Most of Chimera uses AmberTools18 (e.g. minimization; charge addition), but specifically the tools in the Tools→Amber menu use functionality provided by sleap, which is not distributed with current versions of AmberTools. Those tools use AmberTools 1.5, which was released in 2011.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera's users,
I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release?
Best regards, Victor _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Eric Pettersen -
Victor Nazarychev