AMBER Archive (2005)

Subject: RE: AMBER: masks in ptraj - Hbond analysis

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Sep 06 2005 - 15:13:50 CDT


Dear Fabien,

> The first thing is that in that script, for the donor atoms, it is
> looking for GLU_at_OD1 or GLU_at_OD2 instead of
> GLU_at_OE1 and GLU_at_OE2 (but this is a minor problem easy to
> change in the
> script).

There were no GLU residues in the molecule in the tutorial this is why I
never bothered to check if everything was correct. Thus my warning is... If
you use these scripts for your own work make sure you check them thoroughly
before using... (I will update the tutorial nonetheless).

> The real problem I encountered deals with histidines. In my
> molecule, I
> only have 4 HID. When I use the script, I had this
> weird message :

Similarly there are no Histidines in the tutorial molecule so again I never
bothered to add the histidine definitions correctly.

Looking at your error I'm not sure what is going on, I can't see why the
mask would be wrong, it should give the same number of atoms. Unless
something is amiss with the atom naming in your system. Create a pdb with
ambpdb and check that each HIE has only one NE2 and one HE2. If that is true
then perhaps something strange is going on with ptraj's mask selection.

Sorry I can't help much more.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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