Dear amber users,
I want to select all the hydrogens in the protein (216 residues) that are
bonded to nitrogen atoms to function as acceptors in the PTRAJ hydrogen
bond facility. The donors will be the oxygens of the water molecules. I set
the following (erroneous) ptraj script:
*trajin dcd 1 10000 10
acceptor mask :1-216.N= :1-216.H=
hbond distance 3.5 angle 120.0 solventneighbor 6 solvent donor WAT O time
20.0 series hbond_series*
Ptraj complains:
*PTRAJ: acceptor mask :1-216.N= :1-216.H=
Mask [:1-216.N*] represents 244 atoms
Mask [:1-216.H*] represents 1500 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :1-216.N* and :1-216.H* which contain 244
and 1500
atoms respectively. Ignoring...*
Is there a one line to describe all the acceptors in the protein or do I
have to list all the possible nitrogen-hydrogen pairs moieties?
Any help is greatly appreciated!
Jose M. Borreguero
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Received on Sat May 07 2011 - 12:30:04 PDT
