Re: [AMBER] FEW TI and calulation absolute free energy using soft core

From: Cockroft, Nicholas T. <cockroft.1.buckeyemail.osu.edu>
Date: Tue, 18 Oct 2016 19:50:37 +0000

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 - 13:00:02 PDT
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