[Chimera-users] the version of Ambertools that are used in the command "Write prmtop"?

[Victor Nazarychev]

Eric,

Thank you for your answer!

Victor

пн, 8 нояб. 2021 г. в 22:19, Eric Pettersen <pett at 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 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,
> Victor
>
> ср, 27 окт. 2021 г. в 20:58, Eric Pettersen <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.
>>
>> --Eric
>>
>> On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <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,
>> Victor
>>
>> вт, 26 окт. 2021 г. в 20:14, Eric Pettersen <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
>>>
>>>         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> 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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>>>
>>
>
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