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.O
donor mask :1-35.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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Received on Wed Feb 25 2009 - 01:18:55 PST
