Here for hbond analysis I used the following input file
trajin md2.mdcrd
donor :MET50.H
donor :PHE453.H
donor :GLY455.H
donor :GLY457.H
donor :LEU459.H
donor :GLU476.H
donor :CYS499.H
donor :GLN535.HE21
donor :ARG620.HE
donor :ARG620.HH21
donor :ARG878.HE
donor :ARG878.HH21
donor :ARG878.HH21
donor :ARG878.HH21
donor :ARG878.HH22
donor :ASN882.HD2
donor :DRG905.H15
donor :DRG905.H16
donor :DRG905.H25
donor :DRG905.H27
acceptor :GLU52:OE1
acceptor :ILE475:O
acceptor :GLU476:OE1
acceptor :SER454:O
acceptor :DRG905:O12
acceptor :PHE495:O
acceptor :DRG905:O9
acceptor :DRG905:O8
acceptor :GLU574:OE1
acceptor :GLU574:OE1
acceptor :DRG905:O6
acceptor :GLU52:OE1
acceptor :DRG905:O5
acceptor :DRG905:O6
acceptor :GLU52:OE2
acceptor :DRG905:O5
acceptor :ASN882:OD1
acceptor :DRG905:O7
acceptor :ILE475:O
acceptor :SER454:O
hbond distance 3.5 angle 120.0 includeself donor acceptor neighbor 2 series
While running the command
prtaj 3pta_DRG_solvated.top <ptraj_hbond.in>ptraj_hbond.out
I got the following error
PTRAJ: acceptor :ASP498.OD2
WARNING in ptraj, acceptor: error in specification of res/atom selection
PTRAJ: acceptor :Gly574.OE1
WARNING in ptraj, acceptor: error in specification of res/atom selection
PTRAJ: hbond distance 3.5 angle 120.0 includeself donor acceptor neighbor 2
series \ hbondWARNING in ptraj(), hbond: No list of hbond donors/acceptors
has been
specified. Ignoring command...
[No output trajectory specified (trajout)]
md1.mdcrd: 65477 frames.
md1.mdcrd: 65477 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 130954 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (md1.mdcrd) is an AMBER trajectory with 65477 sets
File (md1.mdcrd) is an AMBER trajectory with 65477 sets
*NO OUTPUT COORDINATE FILE WAS SPECIFIED*
*NO ACTIONS WERE SPECIFIED*
Processing AMBER trajectory file md1.mdcrd
Kindly guide me debugging the error.
Regards
Arunima
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Received on Fri Jun 06 2014 - 00:00:02 PDT
