RE: AMBER: masks in ptraj - Hbond analysis

From: Ross Walker <>
Date: Tue, 6 Sep 2005 13:13:50 -0700

Dear Fabien,

> The first thing is that in that script, for the donor atoms, it is
> looking for GLU.OD1 or GLU.OD2 instead of
> GLU.OE1 and GLU.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

|\oss Walker

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

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Sep 06 2005 - 21:53:00 PDT
Custom Search