AMBER Archive (2009)

Subject: [AMBER] (no subject)

From: Beale, John (jbeale_at_stlcop.edu)
Date: Tue Feb 24 2009 - 05:59:51 CST


I am doing MD on a 35-residue peptide in explicit water and I want to
determine the water interactions with donors and acceptors. Below is my
hbond.in file:

 

trajin N390Smd2.mdcrd

donor mask :1-35_at_O

donor mask :1-35_at_N

acceptor TYR N H

acceptor SER N H

hbond distance 3.5 angle 120.0 solventneighbor 6 solventdonor WAT O
solventacceptor WAT O H1 solventacceptor WAT O H2

 

The "hbond" line is the same as found at the bottom of page 102 of the
AmberTools manual. When I try to run ptraj with this input file I get a
segmentation fault.

 

Can anyone tell me what I am doing wrong?

 

Thanks!

 

John Beale

 

 

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