AMBER Archive (2008)

Subject: AMBER: RE: Problem with the NEB tutorial

From: Ross Walker (
Date: Thu Nov 06 2008 - 13:24:30 CST

Hi Hiroshi,

I am copying this to the Amber mailing list so others can see this message
as well.

> I am now trying to use the nudged elastic band module in Amber,
> and examined your tutorial
> but I got a problem. I generated the topology file from the
> struct1.pdb in the above web site (I attached it here), but
> it is different from what you provided. I think the amber
> version and the force field is the same. Could you suggest
> what goes wrong?

I checked the differences between the str1.prmtop file on the website and
the one you sent me. The only differences are in the dihedrals which if you
break them out are backbone dihedrals. Thus I think the origin of the
difference lies with this bugfix:

********>Bugfix 5:
Author: Yong Duan
Date: 06/02/2006

Programs: Anything using the ff03 force field

Description: There is a bad line in frcmod.ff03 in Amber 9. Any prmtop
             files created using this will have to be re-made.

Fix: apply the following patch to amber9/dat/leap/parm/frcmod.ff03


So there are two possibilities here. Either 1) you are using a version of
amber 9 which doesn't have this bugfix applied or 2) I created the
str1.prmtop file in the tutorial before this bugfix was released.

I am not sure which one applies here so if you can let me know if you
applied the bugfixes or not this will explain whether I need to update the
tutorial. Once I hear back from you I'll probably just add a note to the
tutorial page about the bugfix and that (if I did it before the bugfix) the
answers you get might be slightly different because of this but will still
serve as a suitable example. Or alternatively that before running the
tutorial you 'must' make sure you applied this bugfix.

Anyway please let me know and I'll update the tutorial.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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