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
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