[gmx-users] Re: steroid topology

[dhruva chakravorty]

Hi Diane

Thanks for writing in. I guess I should have mentioned
this earlier. To obtain partial charges for my
substrate topology, I do an abinitio calculation
(B-3LYP/6-31G*) and get the Chelpg and MKS charge
distributions using Gaussian. Then I try and fit these
charges to the steroid based on (1) previously defined
GROMOS topologies (2)  The charge group formulation. 

I am fairly confident of my selection of atom types,
bond types and bond angles. To be honest I did these
parts on my own. The selection of improper and proper
dihedrals remains a primary concern for me. It is
primarily for this that I used the PRODRG server. 

I generally do a steepest descenet energy minimization
followed by 5 ps of MD (with gradually reduced
restrainsts), and I repeat this for about 100ps to
equilibrate the protein.  It is when I take off all
restraints and run the final MD (after energy
minimization without restraints) that i see weird
artifacts coming in. I have tried different topologies
with varying dihedrals and have seen weird things. I
will really appreciate it if you could provide me with
a topology you have previously used for a steroid,
especially the section on proper and improper
dihedrals.

With regards

Dhruv

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com