Re: hydrogens collapsing

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Jan 18 2005 - 10:23:40 CST

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 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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