AMBER Archive (2005)

Subject: AMBER: ptraj-acceptor mask format

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Mon Jul 25 2005 - 14:10:47 CDT

All:

I'm trying to use ptraj to locate hydrogen bonds in a protein. If I
use a file containing the lines:

1GJN.top
trajin 1GJN.crd
donor mask :*@OH
acceptor LYS N H
hbond distance 10.0 angle 0.0
go

or

1GJN.top
trajin 1GJN.crd
donor mask :*@OH
acceptor mask :LYS_at_N :LYS_at_H
hbond distance 10.0 angle 0.0
go

I find all 'hbonds' shorter than 10 angstroms (OK, 10 is
ridiculous...I'm just trying to get it to work/show some output). Also,
ptraj finds the correct number of donors and acceptors

But if I try

1GJN.top
trajin 1GJN.crd
donor mask :*@OH
acceptor mask :*@N :*@H
hbond distance 10.0 angle 0.0
go

or

1GJN.top
trajin 1GJN.crd
donor mask :*@OH
acceptor mask :1-153_at_N :1-153_at_H
hbond distance 10.0 angle 0.0
go

ptraj finds the correct number of donors but it can not find any
acceptors (and there should be at least 1 acceptor based on the ptraj
scripts that work).

So, the problem seems to be with the mask in the acceptor line and it
does not seem to like the wild card or range specifications. (But, a
wild card/range works with the mask for the donor command so it would
seem that I've got the format of the mask command correct.) So,
assuming I do have the format correct, why, with the acceptor command,
can't I specify/use a wild card or range with mask?

Pete
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