[Chimera-users] the version of Ambertools that are used in the command "Write prmtop"?
pett at cgl.ucsf.edu
Mon Nov 8 11:19:16 PST 2021
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.
> On Nov 8, 2021, at 10:35 AM, Victor Nazarychev <nazarychev at 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,
> ср, 27 окт. 2021 г. в 20:58, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at 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.
>> On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev at imc.macro.ru <mailto:nazarychev at 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,
>> вт, 26 окт. 2021 г. в 20:14, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at 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 Pettersen
>> UCSF Computer Graphics Lab
>> > On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users <chimera-users at cgl.ucsf.edu <mailto:chimera-users at 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
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