It's difficult to say without seeing your system. Can you send me
off-list the topology and restart file and I'll try to reproduce your
issue? Thanks,
-Dan
On Fri, Oct 20, 2017 at 4:13 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Oct 20 2017 - 12:00:03 PDT
