AW: Newbie's question

From: Norman Geist (
Date: Tue Aug 07 2012 - 00:25:25 CDT

Hi Theresa,


as protein simulation with quantum chemistry is almost not possible because of the required computing power, you will have to cope with classical MD. If your reaction relies on covalent bonding, you can either ignore the covalent part and simulate the rest of the interaction (hydrophobic, hydrophilic, electrostatic, vdw etc.) or use the QMMM hybrid method which for newbs IMHO is too difficult.


To your other questions:

1. Answered above I guess.

2. Yes, if the protein doesn’t consist of only standard amino acids, you will have to find or/and generate parameters for them. How to do this is explained in the force fields itself (Amber,Charm). NAMD is only a implementation that uses the force fields but hasn’t something to do with the parameterization.

3. This depends on the number of atoms that will be in the simulation boxes. For only this project, you could cope with a small CUDA PC about 1000€. Or get access to a high performance computing centre or a cluster. I think at least you will need something about 2TeraFlop/s to get results in a reasonable time.


Norman Geist.


Von: [] Im Auftrag von Theresa H
Gesendet: Montag, 6. August 2012 19:41
Betreff: namd-l: Newbie's question


Dear all

I am a protein crystallographer with interest in MDS. Since we don't have any computational biologist in the department, I want to ask a few basic questions.

I have the structures of two membrane proteins (protein C and D) and one soluble protein (protein B). Protein A can interact with protein C or D through protein B. The protein D also has a domain similar to protein B. Therefore I am interested in knowing why the protein A can't interact directly with protein D.

1. Is NAMD the right tool to answer this question?
2. If so, do I need anything else apart from the crystal structures?
3. How much computational resource is needed?

Thank you.

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