hydrogens collapsing

From: lc_at_chem.au.dk
Date: Tue Jan 18 2005 - 08:46:23 CST


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

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

Thanks in advance


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