[Chimera-users] the version of Ambertools that are used in the command "Write prmtop"?
nazarychev at imc.macro.ru
Mon Nov 8 10:35:45 PST 2021
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"?
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
> On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <nazarychev at imc.macro.ru>
> 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>:
>> 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> 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 at cgl.ucsf.edu
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