RE: AMBER: DNA Tutorial

From: Ross Walker <>
Date: Fri, 18 Feb 2005 17:15:31 -0800

Dear Dwayne,

> I am following the instructions given in the DNA
> tutorial using Amber 8 in linux. The problem I am
> having is that the solvatebox command puts waters only
> at the end of the DNA structure rather than all around
> it. Also, the addions command only puts ions on the x
> - axis in the .inpcrd file. How can one correct this?

This sounds like a possible bug, probably related to the compiler used.

Can you:

1) See if all the amber8 test cases in $AMEBRHOME/test work correctly.

2) Let me know the specs of your machine: cpu, OS, compiler versions etc.
Also if you can post your config.h file from you $AMBERHOME/src dir that
would be useful.

3) Let me know the exact sequence of commands you are using. From initially
firing up leap to solvating it and finding out it has solvated incorrectly.

Hopefully with this information we can nail down your problem.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Sat Feb 19 2005 - 01:53:00 PST
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