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.OD1 or GLU.OD2 instead of
GLU.OE1 and GLU.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.NE2 :HIE.HE2
Mask [:HIE.NE2] represents 20 atoms
Mask [:HIE.HE2] represents 56 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :HIE.NE2 and :HIE.HE2 which contain 20
and 56
atoms respectively. Ignoring...
PTRAJ: acceptor mask :HID.ND1 :HID.HD1
Mask [:HID.ND1] represents 4 atoms
Mask [:HID.HD1] represents 4 atoms
PTRAJ: acceptor mask :HIP.ND1 :HIP.HD1
Mask [:HIP.ND1] represents 4 atoms
Mask [:HIP.HD1] represents 34 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :HIP.ND1 and :HIP.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.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________
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Received on Tue Sep 06 2005 - 12:53:00 PDT
