AMBER Archive (2005)

Subject: AMBER: ptraj Hbond analysis

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Wed Nov 16 2005 - 22:28:52 CST


Dear AMBER users
 
 I have used ptraj to do some hbond analysis of an MD trajectory.
 I have some doubts about the results. The %occupied is greater than 1000 in many cases of solvent acceptor and solvent donor when the imaged trajectory is used.
 When the original trajectory is used the %occupied is around 700 in many cases.
 From the mail archive I understand that it means about 10 / 7 water molecules are hydrogen bonded to the particular atom.
 Is it normal?
 Which one is the correct method? The output obtained is attached.
 
 My input script is
 -----------------------------------------------------------------------------------------------------------------------
 # hydrogen bond analysis
 
 # Read in trajectory
 
 trajin ../ade1l_md9.mdcrd
 trajin ../ade1l_md10.mdcrd
 trajin ../ade1l_md11.mdcrd
 trajin ../ade1l_md12.mdcrd
 ..
 ..
 trajin ../ade1l_md30.mdcrd
 
 
 center:1-8 mass origin
 image origin center
 
 center:1-17 mass origin
 image origin center
 
 rms first mass out rms:1-17
 
 prnlev 3
 
 #
 # backbone + sugar
 #
 donor mask @O1P
 donor mask @O2P
 donor mask @O3'
 donor mask @O5'
 donor mask @O4'
 
 acceptor mask :8_at_O3' :8_at_H3T
 acceptot mask :17_at_O3' :17_at_H3T
 acceptor mask :1_at_O5' :1_at_H5T
 acceptor mask :9_at_O5' :9_at_H5T
 
 #
 # minor groove
 #
 donor RG N3
 donor RG5 N3
 donor RG3 N3
 
 donor RA N3
 
 donor RC O2
 donor RC5 O2
 donor RC3 O2
 
 donor RU O2
  
 acceptor RG N2 H22
 acceptor RG3 N2 H22
 acceptor RG5 N2 H22
 
 #
 # major groove
 #
 donor RG O6
 donor RG5 O6
 donor RG3 O6
 
 donor RG N7
 donor RG3 N7
 donor RG5 N7
 
 donor RA N7
 
 acceptor RA N6 H62
 
 donor RU O4
 
 acceptor DC N4 H42
 acceptor DC3 N4 H42
 prnlev 0
 
 hbond out ade1l_hbond_wat.out \
 solventdonor WAT O \
 solventacceptor WAT O H1 \
 solventacceptor WAT O H2 \
 time 1.0 angle -1.0 distance 3.5

 ==================================================================
   Thanks in advance
 
 Mathew
 

/\/\athew

Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
M.G.University
Kottayam, Kerala
India

email mathew_kvarghese_at_yahoo.co.in

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