Re: [AMBER] How to build a TT dimer

From: M. L. Dodson <>
Date: Thu, 24 Jun 2010 09:11:06 -0500

On Jun 23, 2010, at 9:40 PM, Shi Choong wrote:

> Hello,
> The structure I am doing now contains cyclobutane pyrimidine dimer (CPD)
> lesion that is not available in xleap. So I plan to run the MD simulations
> by replacing the CPD with TT dimer for now. However, there are 2 problems.
> 1) I don't see the coordinates for the CPD atoms on pdb file.
> 2) Does anyone know how to build a TT dimer?
> By chance, is there an amber tutorial related to this type of structure that
> has both DNA and protein?
> Shi

I can't help you on identification of the CPD in the pdb file except to suggest that you visualize the pdb with, e.g., VMD and look for the characteristic kink in the DNA structure at the CPD site.

I am semiretired and had planned to generate some residue descriptors to contribute back to the project and to keep the boredom down during my retirement. I have a TT-dimer residue descriptor I did quite a few years ago (but never published anything using it), and had planned to redo it to the current standards as one of the retirement projects. As it exists now it would not meet modern standards. I gladly yield this field to you, though, as I had and have no plans to publish anything with it. I suggest we conduct an email exchange off line to go through the details of the project, if you are interested. I will send you my notes planning the project (which are in some parts quite detailed). I should say a couple of things about this project, though:

I have outlined in my notes a quite complex and advanced project. Certainly there are ways to do it that are less comprehensive than I had planned. Only you can know the level appropriate for your overall project. So think about that aspect.

If you are unfamiliar with new residue generation for AMBER and do not have ready access to someone with that experience, or even if you do, I suggest you study the papers for at least the ff94 (particularly nuc94), ff99 and ff99SB, GLYCAM-06, and parmbsc0 force fields as referenced in Chapter 2 of the AmberTools-1.4 manual. I suggest you also visit the REDD web site (linked off the main AMBER web page) and read all the documentation there and go through their tutorials. Be prepared to do quite a few quantum chemistry calculations (with Gaussian or GAMESS or their equivalent; I don't think mopac or sqm can do the constrained structure optimizations you will need to do the project the way I have it planned in my notes, and certainly most versions of mopac cannot do calculations at an appropriate level of representation).

Unless you are an experienced AMBER user I might gently suggest another residue descriptor project as a learning exercise before tackling this (see the tutorials on the AMBER and antechamber web sites). A CPD descriptor is not a good learning project. Trust me on this, it was my learning project and it took me about a year (with MANY restarts) before I had any confidence at all in the results. (I did not have ready access to experienced AMBER users, so am almost completely self-taught.) I was fortunate enough to have the spare time to go through such an extensive self-teaching procedure. At the least, go through every tutorial you can find if you have not done something like this before.

Let me know if you are interested in pursuing this further.

Bud Dodson
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Thu Jun 24 2010 - 07:30:05 PDT
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