Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4.

From: case <>
Date: Tue, 22 Jun 2010 18:30:00 -0400

On Wed, Jun 23, 2010, Catein Catherine wrote:
> Start with the same pdb file, I startup the xleap in amber10
> Ambertool1.2 with the following commands in two different computer.

Can you post the pdb file that has generated so many emails? We are *still*
wondering if it has phosphate atoms on the terminal residues.

> In computer 1, I can read in the pdb file without adding new atoms error
> message appears.
> In computer 2, error message was found in the terminal DNA base pairs.
> e.g. Following errors appears for the first DA.
> Created a new atom named: P within residue: .R<RA5 1>

This is a very weird error message ("RA5"?) unless it is just a typo.

> Created a new atom named: O1P within residue: .R<DA5 1>
> Created a new atom named: O2P within residue: .R<DA5 1>
> I compared the differences between two version of amber10 (same amber10
> tar file as used during installation, but computer 1 was installed 1
> year ago, computer 2 is installed recently. The bugfix.all file used
> in this two installation may be different.). In later case, I found
> $AMBERHOME/dat/leap/parm/frcmod.ff99SB was loaded. However, in the
> first case, it is not.

Again, we need much more exact information. How do you know that
frcmod.ff99SB was not loaded? It sounds like the installation for "computer
2" is damaged. (Even though frcmod.ff99SB applies only to proteins, if it
is missing, there may be lots of other problems as well.)

Try this: on either computer, download AmberTools1.4 into some new directory,
install it, and run you test case from there. And, really think about some
way that you could post at least a part of the pdb file you are using (is it
something you can't share?)


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Received on Tue Jun 22 2010 - 16:00:03 PDT
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