AMBER Archive (2005)

Subject: Re: AMBER: Can GB and MS work correctly together in mmpbsa?

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Mon Jul 18 2005 - 12:31:29 CDT

Why don't you email me directly and show me what modifications you
have done to the code to account for Fl. This is a tricky problem and
you make need some hands on assistance with this.

On 7/16/05, zhli_2000_at_126.com <zhli_2000_at_126.com> wrote:
> Thank you for the advice. I have put the atom radium of F in the
> mm_pbsa_calceneent.pm. Then I run the following :
>
> --------------------------------------------------------------------
> PREFIX min_cyc16
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./mincomplex.top
> RECPT ./ppo.top
> LIGPT ./cyc16.top
> #
> GC 0
> AS 0
> DC 1
> #
> MM 1
> GB 1
> PB 0
> MS 0
> #
> NM 0
> #
> -------------------------------------------------------------------
> The error message is still :
> bad atom type: F
>
> When I switch MS=0 to MS=1, the error message is:
> Checking sanity
> Checking GENERAL
> Energy decomp is not (yet) possible with GC, AS, NM, PB, MS
>
> So I don't know how to deal with this. Which input file can be run
> correctly?
>
> ----------------------------------------------------------------------------
> ---
>
> On Fri, 15 Jul 2005 14:08:43 -0600, Scott Pendley <scott.pendley_at_gmail.com>
> wrote:
>
> > As a follow up to my last note. Specifically you should modify the
> > generate_pqr() section of mm_pbsa_calceneent.pm. This is the
> > modification I added to my code . . .
> >
> > "Na+" => 1.200 + 1.400,
> > "Cl-" => 1.700 + 1.400,
> > "MG" => 1.180 + 1.400,
> > "F" => 1.470 + 1.400,
> > );
> >
> > Have fun with this...
> >
> >
> > On 7/15/05, Scott Pendley <scott.pendley_at_gmail.com> wrote:
> >> That is because you have not put in the parameters of F for the
> >> molsurf program. It is similiar to doing to the modification you did
> >> earlier. If you run into trouble doing this let me know and I will
> >> show you how I did it.
> >>
> >> On 7/15/05, zhli_2000_at_126.com <zhli_2000_at_126.com> wrote:
> >> > Hi,
> >> > Thank you for the explanation. But Because there is an atom F in the
> >> > ligand, when I switch MS=1 to MS=0, mmpbsa cann't work correctly. The
> >> error
> >> > message is:
> >> > bad atom type: F
> >> >
> >> > What should I do?
> >> > Thank you!
> >> >
> >> >
> >> > >
> >> > > If you switch MS=1 to MS=0, it should work. Energy decomposition
> >> does not
> >> > > work so far with a SAS calculation based on MS, but relies on
> >> another
> >> > > method approximating atomic surfaces starting from icosahedra.
> >> > > Best regards
> >> > >
> >> > > Holger
> >> > >
> >> > >>
> >> > >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > -----------------------------------------------------------------------
> >>
> >>
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> >>
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>
>
>
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