I haven't used mcwat very much, so others may be able to offer more help.
Hopefully these will be useful:
I would start by making sure your mcat setup works in standard MD before
trying to combine with TI.
also, I usually put commas after all variable definitions.
try defining mcresstr
On Fri, May 17, 2024 at 3:24 PM Juraj Dobias via AMBER <amber.ambermd.org>
wrote:
> Hi,
>
> I wanted to use Monte Carlo water equilibration
> (https://pubs.acs.org/doi/10.1021/acs.jctc.1c00867) to sample buried
> water molecules in my RBFE calculation. My input settings are:
>
> &cntrl
> nstlim = 250000, dt = 0.002000,
> imin = 0
> ntxo = 1
> ntc = 2
> ntf = 1
> cut = 10
> iwrap = 1
> ntt = 3
> gamma_ln = 2.0
> ntpr = 5000
> ntwr = 50000
> mcwat=1
> nmd = 1000
> nmc = 100000
> mcwatmask = ':L1'
> mcligshift = 12
> irest = 1, ntx = 5
> barostat=2, ntp=1, taup=2
> ntwx=10000
>
> clambda=0.000000
> ifsc = 1
> icfe = 1
> scalpha = 0.5
> scbeta = 1.0
> gti_add_sc = 5
> gti_scale_beta = 1
> gti_cut_sc_on = 8
> gti_cut_sc_off = 10
> gti_lam_sch = 1
> gti_ele_sc = 1
> gti_vdw_sc = 1
> gti_cut_sc = 2
> gti_ele_exp = 2
> gti_vdw_exp = 2
> gti_syn_mass = 0
> scmask1 = ':L1&(.H14)'
> scmask2 = ':L2&(@C17,O3,N5,H14,H15)'
> timask1 = ':L1'
> timask2 = ':L2'
> noshakemask = ':L1,L2'
> /
>
> Simulation stopped with error:
>
> Error in definition of mcres - residue with name does not exist.
>
> I am pretty sure that my mcwatmask is valid. Simulation with mcwat=0 is
> running without issues.
>
> Any help would be appreciated.
>
> Juraj Dobias
>
>
>
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Received on Sat May 18 2024 - 05:00:02 PDT
