AMBER Archive (2006)

Subject: AMBER: generating parameters for the NADH analogue H4NAD

From: Simon Whitehead (SJW084_at_bham.ac.uk)
Date: Thu Feb 23 2006 - 12:31:02 CST

Dear amber users,

I am trying to generate parameters for an analogue of NADH called H4NAD (tetraNAD) which is one the substrates of the enzyme i am running simulations on (AMBER 8). However, I have some questions about how i should go about it using antechamber starting with a pdb file of NADH;

1) How do i modify the pdb to add in the additional hydrogens and alter the hybridisation states of the carbons in the nicotinamide ring?
2) What can i do if GAFF is not able to provide certain parameters for the molecule?
3) Some of the carbon-carbon bond lengths differ from NADH so would i need to say then minimise this structure in order to correct the geometry or would this simply occur when i perform my minimisations on the entire system prior to running dynamics?
4) Which charge method would be the most suitable considering the fact that the molecule has about 70 atoms and also are there any specific variables i should be aware of?

I appreciate i am asking quite a lot here but, I have no experience of generating my own parameters but would like to generate a realistic model because i`m aiming to study the motions of the substrate and interacting active site residues, compared to the physiological substrate, in some detail.

Kindest regards and thanks in advance

Simon whitehead
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