Hello,
Does the distance.in file look okay?
I wanted to confirm with the experts. I think I have imaged the traj file properly...
Regards
From: Debarati DasGupta<mailto:debarati_dasgupta.hotmail.com>
Sent: 24 June 2020 17:54
To: AMBER Mailing List<mailto:amber.ambermd.org>; Daniel Roe<mailto:daniel.r.roe.gmail.com>
Subject: Re: [AMBER] restraint 10 kcal/mol
Hi Daniel,
Thanks for the quick reply.
Yes I have iwrap=1 in my prod input file
This is how my distance input file to cpptraj looks like:
parm post_processed _solvated.prmtop
trajin post_processed_solvated_prod.mdcrd 1 last
center mass origin :1-287
image origin center
reference post_processed_box_SITE1.pdb
strip :WAT
strip :Na+
rms reference mass out backbond_aligned_RMSD.txt :3-286.CA,C,N,O
distance SITE1_stat :EOH point -3.8 13.7 -7.5 out distance_probe.out
go
~
Sent from Mail<
https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: Daniel Roe<mailto:daniel.r.roe.gmail.com>
Sent: 24 June 2020 16:42
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] restraint 10 kcal/mol
One thing to check is if you have imaging artifacts between runs. You
are using iwrap=1 so imaging is on, but restraints do not follow the
minimum image convention, so if your ligand was imaged but your
receptor wasn't that could cause an issue. If that is indeed the
problem, the solutions are to either 1) turn off wrapping (should be
fine if you're using the default netcdf restart/trajectory files) or
2) make sure you 'autoimage' (or somehow otherwise reimage) your
restart files before you use them as input coordinates.
-Dan
On Wed, Jun 24, 2020 at 2:36 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Hi All
> I am a bit confused with regard to the NVT production runs of TI setup I had established a few weeks back.
> My ligand of interest is ethanol and my prod.in file looks like this:
> [SITE1]$ cat ./0.11505/prod_NVT.in
> &cntrl
> imin = 0, nstlim = 20000000, dt = 0.001,
> irest = 1, ntx = 5, ig = -1,
> tempi = 300.0, temp0 = 300.0,
> ntwx = 10000, ntwe = 10000, ntwr = 10000, ntpr = 10000,ntwv=-1, ntave =1000,
> cut = 11.0,
> ntt =3, ntb = 1, ntp = 0, gamma_ln=3, iwrap = 1,
> ntc = 1, ntf = 1, tol = 0.00001,
> nsnb = 10, nscm = 10,
> ioutfm=1,
> taup = 2,
> ntr=1, restraintmask=':EOH', restraint_wt=10.00,
> icfe = 1, clambda = 0.11505, ifsc=1,
> timask1=':EOH',timask2='',
> scmask1=':EOH', scmask2=''
> &end
> &ewald
> skinnb=2, nfft1=96, nfft2=96, nfft3=96,
> /
>
> So, after the run was complete, I was curious to see how far my ligand has translated from its tether point.. and after doing a COM distance cpptraj script run, I find that for 3 lambda values 0.11505, 0.20634, and 0.31608; the ligand has moved around quite a bit as in > 3 Angstroms from its initial solvated state. Is this expected or am I doing something wrong in putting the restraint weight and mask?
> I thought that 10 kcal/mol is quite a big force to keep ligand restrained in the pocket. I was not expecting a 3-4 Angstrom jiggling of the ligand atoms.
> Should I be worried?
> [cid:image001.png.01D64A34.03736FA0]
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 26 2020 - 06:00:07 PDT
