From: lc_at_chem.au.dk
Date: Tue Jan 18 2005 - 12:12:04 CST
Hi,
Alex D. MacKerell published an article about a month ago in Biochemistry (2004,
43, 15318-15328) were cholesterol parameters were given as supporting
material.
Since all atomtypes in estradiol, except the phenol-group, are the same as in
cholesterol, I took it for given they would be correct to use...
/Leyla
Citat Brian Bennion <brian_at_youkai.llnl.gov>:
>
> Hello,
>
> I am a little surprised that you found parameters so similiar to
> estradiol.
>
> There are some parameters missing or more likely they are incorrect. My
> guess is that the H-C-C angle force constant is not large enough to
> balance the H-C-C-X dihedral terms.
>
> Just my $0.02
>
> Regards
> Brian
>
>
>
>
>
> On Tue, 18 Jan 2005 lc_at_chem.au.dk
> wrote:
>
> >
> >
> > Hi,
> >
> > I am trying to simulate a system with the estrogen receptor and its
> natural
> > ligand estradiol (a steroid). I have found cholesterol parameters, which
> > together with the CHARMM prot_lipid forcefield should be able to create
> most
> > steroids.
> >
> > My problem is, that when I try to minimize, heat or whatever I want to do
> the
> > hydrogens are collapsing. Eg. three hydrogens in a methyl group obtains
> same
> > coordinates after about 300 steps of minimization of heating of the
> system.
> >
> > The problem is not with the parameters since I have been able to minimize
> the
> > system using CHARMM without the hydrogens collapsing.
> >
> > Do you have any ideas to what I can do? I can not imagine anything else to
> > try...
> >
> > Thanks in advance
> >
> > Leyla
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
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>
>
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