AMBER Archive (2005)

Subject: AMBER: masks in ptraj - Hbond analysis

From: Fabien Cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Tue Sep 06 2005 - 06:38:11 CDT

Dear all,

I remarked a problem with the masks used in ptraj to perform Hbond analysis.
I used the script found at :
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_eight/index.htm
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).
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 :

PTRAJ: acceptor mask :HIE_at_NE2 :HIE_at_HE2
Mask [:HIE_at_NE2] represents 20 atoms
Mask [:HIE_at_HE2] represents 56 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :HIE_at_NE2 and :HIE_at_HE2 which contain 20
and 56
atoms respectively. Ignoring...

PTRAJ: acceptor mask :HID_at_ND1 :HID_at_HD1
Mask [:HID_at_ND1] represents 4 atoms
Mask [:HID_at_HD1] represents 4 atoms

PTRAJ: acceptor mask :HIP_at_ND1 :HIP_at_HD1
Mask [:HIP_at_ND1] represents 4 atoms
Mask [:HIP_at_HD1] represents 34 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :HIP_at_ND1 and :HIP_at_HD1 which contain 4 and 34
atoms respectively. Ignoring...

In fact, the HID part is correct but it seems that ptraj finds something
for HIE or HIP, which he should not.
I did not manage to find where the mask is processed in ptraj and so I
was not able to see where this problem comes from.

Any help would be appreciated.
Thanks in advance,
Fabien 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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