Thank you so much for these helpful pointers. It took me a little while to
figure out how to set-up all of the simulation files (including using
Parmed to remove redundant residues in the protein). I now run into an
additional problem when trying to run TI, which is that the periodic
boundary conditions seem to "fall apart" and start to form a droplet after
heating during the equilibration phase of the simulation. I don't really
understand why this occurs. I attached my heating control procedure below,
which runs heating at a lambda value of 0.5. Maybe someone could point
me in the right direction. I also checked the last line of the crd file and
it seems to still contain the PBC information (also attached below).
Best,
Wanlei
heating
&cntrl
imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.002,
nmropt = 1,
ntt = 1, temp0 = 300.0, tempi = 5.0, tautp = 1.0,
ntb = 1,
ntc = 2, ntf = 1,
ioutfm = 1, iwrap = 1,
ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,
ntr = 1, restraint_wt = 5.00,
restraintmask='',
icfe = 1, ifsc = 1, clambda = 0.5, scalpha = 0.5, scbeta = 12.0,
logdvdl = 0,
timask1 = ':220', timask2 = ':233',
scmask1 = ':220', scmask2 = ':233'
/
&ewald
/
&wt
type='TEMP0',
istep1 = 0, istep2 = 8000,
value1 = 5.0, value2 = 300.0
/
&wt type = 'END'
/
...
11.3253730 11.6195170 6.2629100 11.2108740 10.5975510 7.3739250
9.5034900 11.8649720 4.2588710 9.0437870 12.6165530 3.8846730
8.8747360 11.1456190 4.2003510 2.6726120 11.0646450 4.2605820
2.9603930 10.8100750 3.3838830 3.1849340 10.5123810 4.8511390
2.7398480 11.9862550 11.6274020 3.6665790 11.7506820 11.6709980
2.7248910 12.8134550 11.1460050 9.3076040 11.2132410 11.4515060
10.1001360 10.7181640 11.2441020 9.6009190 11.8922550 12.0590670
80.3610580 80.7289330 80.3998680 90.0000000 90.0000000 90.0000000
On Fri, Feb 19, 2021 at 10:33 AM David A Case <david.case.rutgers.edu>
wrote:
> On Fri, Feb 19, 2021, WW wrote:
> >
> >I would like to investigate how point mutations in one protein affect the
> >binding affinity of protein-protein interaction using Amber18. Running
> >Amber-TI module as-is results in an error saying that the maximum number
> of
> >softcore atoms is 200.
>
> I'm not sure what sort of calculation you are thinking about here. I'd
> suggest making the softcore region be the amino acid that is mutating.
> Then
> perform the mutation once in the presence of the second protein, then again
> in its absence. The difference will give you an estimate of the effect of
> the mutation on protein-protein binding. There is no need for any large
> softcore region, which you almost certainly do not want.
>
> ....good luck....dac
>
>
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Received on Thu Apr 08 2021 - 16:00:02 PDT
