The idea of FEW is to aid you in setup of _relative_ alchemical free
energy calculations (as well as some end-points methods). Setup of
absolute transformation is trivial at this stage as the manual shows.
The real issue there is how to set up restraints when sampling in
inhomogeneous environments and standard state correction.
On Tue, 18 Oct 2016 19:50:37 +0000
"Cockroft, Nicholas T." <cockroft.1.buckeyemail.osu.edu> wrote:
> I have checked the manual and saw that was the syntax for directly
> running TI. However, the input files for FEW appears to desire a
> different syntax. Specifically, <lig_alias_v0>.<atom name list
> separated by comma>
>
>
> Thus using parameters such as:
>
>
> ti_simulation_setup 1
> charge_method am1
> lig_name_v0_struct struct_name
> lig_name_v1_struct
> lig_alias_v0 struct_alias
> lig_alias_v1
> softcore_mask_v0 ':1'
> softcore_mask_v1 "
>
>
> will yield the error:
>
> ERROR: The 'softcore_mask_v0' information in the command file has not
> the required format.
>
> ERROR: The 'softcore_mask_v1' information in the command file has not
> the required format.
>
>
> The section of the manual on FEW/TIW that has documentation on
> softcore masks references section 22.1 for additional format details.
> Therefore, I was curious if there was an alternative accepted syntax
> by FEW or if there were specific parameters that could be used to
> generate TI input files using FEW that would then contain:
>
> icfe = 1, ifsc = 1,
> timask1=’:1’, scmask1=’:1’,
> timask2=”, scmask2=”,
>
>
>
> ________________________________
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Sent: Tuesday, October 18, 2016 2:58:13 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] FEW TI and calulation absolute free energy using
> soft core
>
> On Tue, 18 Oct 2016 18:20:34 +0000
> "Cockroft, Nicholas T." <cockroft.1.buckeyemail.osu.edu> wrote:
>
> > Hi,
> >
> >
> > I was wondering if it is possible to use the Free Energy Workflow to
> > calculate absolute binding energies using TI. The syntax of the TI
> > setup input file for the scmask appears to preclude empty masks and
> > absent structures for v1. Is there any workaround or different
> > syntax that can be used to get this to work or is directly running
> > the TI calculations the best option?
>
>
> Have you had a look into the manual?
>
> icfe = 1, ifsc = 1,
> timask1=’:1’, scmask1=’:1’,
> timask2=”, scmask2=”,
>
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Received on Tue Oct 18 2016 - 23:30:03 PDT
