I'm not an expert on the TI errors so will let others address that part.
However, I wonder why you are doing the setbox command and editing the
outputs from leap - does the solvateoct alone not produce a usable file?
*A secondary problem I have encountered is when I use a truncated
octahedron for the solvation of the system with solvateOct. I use this
command in leap for the complex and the protein: setBox protein/complex vdw
{ x = y = z }, and then I manually edit the last line of
protein/complex.rst7 and merged_protein/complex.rst7 with the angles a = b
= c = 109.47. When I run the calculation, it halts with Error: ifbox=2 in
prmtop but angles are not correct. Incidentally, when I set ifbox=3 it runs
without this error. Is this an acceptable solution?*
On Mon, Jul 24, 2023 at 12:27 PM Prokopios Andrikopoulos via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER Users,
> I've been trying to do a TI for a mutation (res position 362) on a quite
> large trimer (1125 res per chain with a ligand at each chain at positions
> 3376-3378 - the ligand associated to the mutation is at 3378). I'm using
> ff14sb with TIP3P via the Amber 22 pmemd.cuda and the parmed from Amber 18
> (v22 parmed does not work on my cluster installation atm). I've adapted the
> relaxation regime from tutorial 3.1, by changing ntmin=2, ntf=1 and ntp=1
> to make it acceptable for TI. I do a minimization > slow heating > and a
> series of 1ns constant pressure runs (with one more minimization
> in-between) releasing slowly the restrains as in tutorial 3.1. The
> relaxation regime works without any problems without the TI keywords (icfe,
> clambda etc.) on the normal prmtop using either a box or truncated
> octahedron for solvation. When I prepare the dual topology parm+rst7 is
> where the problems start. My parmed command is: tiMerge :1-3377 :3378-6754
> :362 :3739. Parmed moves the mutated res in the merged files right after
> the 1st chain, so in the relaxation inputs I have to point to 1126 instead,
> with the associated ligand at 3379.
>
> While the normal relaxation w/out TI reports a normal Density of ~1.00,
> the TI calculations density is reported in the 0.12-0.25 range in the
> constant pressure runs. A difference in energy is also evident in the
> initial minimization between the normal system and the TI complex with λ =
> 0.0: i.e. after 1000 min steps, this is EAMBER = -2180402.3012 and
> -2171818.4624 for the normal and TI calculation, respectively.
> Below are inputs for the complex with λ = 0.0. The input for the constant
> pressure run is the 4th in the regime with reduced backbone restrains. This
> fails for all λ values at 65-%75% of the total steps with the ERROR:
> Calculation halted. Periodic box dimensions have changed too much from
> their initial values. I would appreciate any help with this problem, and I
> can provide more details for the calculations.
>
> A secondary problem I have encountered is when I use a truncated
> octahedron for the solvation of the system with solvateOct. I use this
> command in leap for the complex and the protein: setBox protein/complex vdw
> { x = y = z }, and then I manually edit the last line of
> protein/complex.rst7 and merged_protein/complex.rst7 with the angles a = b
> = c = 109.47. When I run the calculation, it halts with Error: ifbox=2 in
> prmtop but angles are not correct. Incidentally, when I set ifbox=3 it runs
> without this error. Is this an acceptable solution?
>
> minimisation
> &cntrl
> imin = 1, ntmin = 2, maxcyc = 10000,
> ntpr = 50, ntwe = 0, ntwr = 500,
> ntb = 1, ntp = 0, ntf = 1, ntc = 2,
> ntx = 1, ntr = 1, ioutfm = 1, ntxo = 2,
> cut = 10.0,
> restraintmask = ':1-3379',
> restraint_wt = 100.,
>
>
> icfe = 1, ifsc = 1, clambda = 0.0, scalpha = 0.5, scbeta = 12.0,
> logdvdl = 0,
> timask1 = ':362', timask2 = ':1126',
> scmask1 = ':362', scmask2 = ':1126',
> /
>
> &ewald
> /
>
>
> heating to 298K
> &cntrl
> imin = 0, nstlim = 1000000, irest = 0, ntx = 1, dt = 0.001,
> ntt = 3, temp0 = 298.0, tempi = 100.0, tautp = 1.0, ig = -1,
> ntc = 2, ntf = 1,
> ntb = 1, ntp = 0, tol = 0.00001,
> ioutfm = 1, iwrap = 0, ntxo = 2, nscm = 0, cut = 8.0,
> ntwe = 0, ntwx = 10000, ntpr = 1000, ntwr = 1000,
>
> nmropt = 1, gamma_ln = 1.,
> ntr = 1, restraint_wt = 100.,
> restraintmask=':1-3379',
>
> icfe = 1, ifsc = 1, clambda = 0.0, scalpha = 0.5, scbeta = 12.0,
> logdvdl = 0,
> timask1 = ':362', timask2 = ':1126',
> scmask1 = ':362', scmask2 = ':1126',
> /
>
> &ewald
> /
>
> &wt
> type='TEMP0',
> istep1 = 0, istep2 = 1000000,
> value1 = 100., value2 = 298.
> /
>
> &wt type = 'END'
> /
>
> 4th constant pressure run of 1ns
> &cntrl
> imin = 0, nstlim = 1000000, dt = 0.001,
> irest = 1, ntx = 5, ig = -1,
> temp0 = 298.0,
> ntc = 2, ntf = 1,
> ntwx = 10000, ntwe = 0, ntwr = 1000, ntpr = 1000,
> cut = 8.0, iwrap = 0,
> ntt = 3, gamma_ln = 1.0, ntb = 2, ntp = 1, barostat = 2,
> nscm = 0,
> ntr = 1, restraintmask = ".CA,N,C", restraint_wt = 1.
> ioutfm = 1, ntxo = 2,
>
> icfe = 1, ifsc = 1, clambda = 0.0, scalpha = 0.5, scbeta = 12.0,
> logdvdl = 0,
> timask1 = ':362', timask2 = ':1126',
> scmask1 = ':362', scmask2 = ':1126',
> /
>
> &ewald
> /
>
>
> Thanks for any suggestions
> P. A.
>
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Received on Mon Jul 24 2023 - 10:00:02 PDT
