Hi,
I've tried autoimage with no luck :(
Also tried the following but although the coordinates are shifted, the glycoprotein atoms are still outside the water box:
1. Just centering using mass of glycans on outside of protein:
parm CDOM_CPLX_Neut_Sol_rnb.prmtop
trajin md1_rnb.rst7
center :0fA,0SA,2MA,3LB,4YB,UYB,VMB mass
image center :0fA,0SA,2MA,3LB,4YB,UYB,VMB
trajout md1_rnb_glyccentered.rst7
go
quit
2. Centering using only mass of protein:
parm CDOM_CPLX_Neut_Sol_rnb.prmtop
trajin md1_rnb.rst7
center :1-589 mass
image center :1-589
trajout md1_rnb_prot_centered.rst7
go
quit
3. Centering using mass of glycans and protein residues together:
parm CDOM_CPLX_Neut_Sol_rnb.prmtop
trajin md1_rnb.rst7
center :1-661 mass
image center :1-669
trajout md1_rnb_glycprot_centered.rst7
go
quit
Any ideas what might be going wrong?
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
________________________________________
From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Sent: 19 October 2017 06:14:32 PM
To: david.case.rutgers.edu; AMBER Mailing List
Subject: Re: [AMBER] Protein drift from solvent box
Thanks David, I will try autoimage again and report back.
Just to clarify, do you mean 10A is rather short for the solvent-solute barrier or non-bonded distance?
_____________________________
From: David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>>
Sent: Donderdag, Oktober 19, 2017 6:11 nm.
Subject: Re: [AMBER] Protein drift from solvent box
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
On Thu, Oct 19, 2017, Lizelle Lubbe wrote:
I thought that 10A was commonly used for the non-bonded cutoff distance
and to avoid the computational cost of extra waters I chose 10A instead of
12A for the barrier distance.
10 Ang is pretty short; 12-14 Ang would be some better, but that's mostly a
recommendation for future work, i.e. you probably don't need to re-do the
simulations you already have.
>
> Could you please explain to me why this is incorrect and how it would
> cause shrinkage of the box?
What you did sounds fine.
>
> I measured the glycan-glycan distance between neighbouring periodic
> images after 8ns production and during the simulation it ranges between
> 25-70A. Does this mean that the protein drift is just an imaging issue
> or can the molecules start interacting later on?
The protein drift should be just an imaging problem. See if running autoimage
followed visualization looks OK.
....dac
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Received on Fri Oct 20 2017 - 01:30:01 PDT
