AMBER Archive (2006)

Subject: RE: AMBER: Zn metal library

From: Ross Walker (
Date: Mon Nov 06 2006 - 00:08:20 CST

Hi Fenghui,

> Simulating a Solvated Protein that Contains
> Non-Standard Residues.
> Now this tutorial has been deleted. Does this means
> that this method is not so valuble?

The tutorial has not 'strictly' been deleted. It is still available here:
The reason I have removed it from the official list is that I plan on
replacing it with a more indepth tutorial that shows one how to setup a more
complex system. I plan to show LADH, with NADH a zinc, two cysteines,
n-cyclohexyl formamide and a histidine. However, it is likely going to be a
while until I find the time to get this done.

> I have a protein contains four Zn, each Zn is
> cordinated by 4 Cys. Can we say that if we use the
> protocol in "Simulating a Solvated Protein that
> Contains Non-Standard Residues", only one Zn library
> file from one specific Cys can be used for all of the
> 4 Cys for the MD file construction?

There are a huge number of different ways in which you can approach this
problem. The question comes down to how much of a thorough job you want to
do. At the one end you can just create a zinc residue containing just zinc,
give it a charge of 2+ and then don't bother bonding it to any residues
explicitly. At the other end you can try creating zinc with ACE and NME
capped cysteine's around it and fitting their charges with RESP. Then you
can create 4 individual cysteine residues (say CYA, CYB, CYC and CYD) and
modify their charges and atom types / parameters as necessary. Then create a
zinc residue with a type - say ZNS and give it the resp charge you
calculated. Then bond it to each of the cysteines and provide all the
missing parameters.

The second option is really the recomended one but is quite involved.

> If you do not recommend the simple method, will you
> please introduce the basic steps to get the files of
> Zin by R.E.D or some other programs to get the small
> molecule files?

See above. The main object of the tutorials is just to get you familiar with
how the various parts of Amber work, how they interconnect, how you modify
things etc. Beyond this once you get into more advanced territory my best
advice is to try it out for yourself. Once the tutorials have given you the
basic building blocks you should be able to use these in a more complex
fashion to deal with advanced systems. I taught myself how to build all of
LADH during my PhD without the aid of any tutorials or anybody showing me
how to do it. I simply read the manual and then experimented. I highly
recommend that you try the same thing. The big advantage of a computer over
working in the lab is that you won't kill yourself if what you do ends up
going wrong ;-).

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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