Re: [AMBER] mdgx CreateBellyMask error

From: David Cerutti <dscerutti.gmail.com>
Date: Mon, 15 Apr 2019 11:02:08 -0400

It looks like the failure actually happens in the &ipolq namelist, as mdgx
will dive in there and take those directives if one is supplied. The
'solute' keyword is telling mdgx to hold residue 1 (:1) fixed, but there is
more to your solute (blocked dipeptide = 3 residues). So say solute ':3'
and that should work.

Dave


On Mon, Apr 15, 2019 at 10:50 AM Anthony Bogetti <anthony.bogetti.gmail.com>
wrote:

> Hello,
>
> I'm trying to run mdgx with a blocked dipeptide. I've done this
> successfully before, but now the program runs for about two seconds then
> fails with the following error message:
>
> CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
> CreateBellyMask >> controls a constraint group and is mobile, but
> CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
> CreateBellyMask >> constraint group, is not mobile.
> CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
> CreateBellyMask >> controls a constraint group and is mobile, but
> CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
> CreateBellyMask >> constraint group, is not mobile.
> CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
> CreateBellyMask >> controls a constraint group and is mobile, but
> CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
> CreateBellyMask >> constraint group, is not mobile.
> CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
> CreateBellyMask >> controls a constraint group and is mobile, but
> CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
> CreateBellyMask >> constraint group, is not mobile.
> CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
> CreateBellyMask >> controls a constraint group and is mobile, but
> CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
> CreateBellyMask >> constraint group, is not mobile.
> CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
> CreateBellyMask >> controls a constraint group and is mobile, but
> CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
> CreateBellyMask >> constraint group, is not mobile.
> CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
> CreateBellyMask >> controls a constraint group and is mobile, but
> CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
> CreateBellyMask >> constraint group, is not mobile.
> CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
> CreateBellyMask >> controls a constraint group and is mobile, but
> CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
> CreateBellyMask >> constraint group, is not mobile.
>
> I don't know what this means.
>
> Here's my mdgx input script (the &cntrl portion):
>
> &cntrl
> imin = 0
> irest = 0
> dt = 0.002
> nstlim = 250000
> ntp = 0
> ntt = 3
> tempi = 298.0
> temp0 = 298.0
> gamma_ln = 1.0
> * rigidbond = 1*
> rigidwat = 1
> es_cutoff = 10.0
> vdw_cutoff = 10.0
> ntpr = 500
> ntwr = 250000
> ntwx = 500
> iwrap = 1,
> &end
>
> If I remove the rigidbond =1 line it runs just fine. However, I would like
> to keep that in.
>
> I have attached my (solvated) topology and coordinate files and the full
> mdgx input for reference.
>
> Thanks,
> AB
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Received on Mon Apr 15 2019 - 08:30:03 PDT
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