# [AMBER] evaluating hydrogen bond using ptraj

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Fri, 11 Jul 2014 07:31:05 +0100

I am using ptraj to evaluate hbond for glycolipids in bilayer system in water. The glycolipid that I use have 11 oxygens (O11,O12,O13,O14,O15,O16,O22,O23,O24,O25,O260 and 7 hydroxyl groups (O12-H12,  O13-H13, O16-H16, O22-H22, O23-H23, O24-H24, O26-H26).

I wish to calculate the hydrogen bond between the lipids only (inter-molecular hydrogen bonding) for 64 lipids. So I defined the donor and acceptor as below:

trajin  \$path/\$system-reimage-set60.traj

###############################
donor mask :1-64.O11,O12,O13,O14,O15,O16,O22,O23,O24,O25,O26

acceptor mask :1-64.O12 :1-64.H12
acceptor mask :1-64.O13 :1-64.H13
acceptor mask :1-64.O16 :1-64.H16
acceptor mask :1-64.O22 :1-64.H22
acceptor mask :1-64.O23 :1-64.H23
acceptor mask :1-64.O24 :1-64.H24
acceptor mask :1-64.O26 :1-64.H26

hbond distance 3.5 angle 120.0 out HB_inSameLayer_001_064.tbl

This produce a table and I calculated the hydrogen bonding fraction by adding column \$10 and divide by 100% and divide with number of lipids involved that is 64.
Is this method correct for calculating the inter-molecular hydrogen bond using ptraj?

Next, I wanted to calculate the hydrogen bond between water (1556 molecules) and 64 lipids (solvent & solute).

As a first step, I defined oxygen from water as a donor and hydroxyls from lipids as acceptors. The command is shown below:

trajin  \$path/\$system-reimage-set60.traj

###############################
donor mask :257-1556.O

acceptor mask :BMR.O12 :BMR.H12
acceptor mask :BMR.O13 :BMR.H13
acceptor mask :BMR.O16 :BMR.H16
acceptor mask :BMR.O22 :BMR.H22
acceptor mask :BMR.O23 :BMR.H23
acceptor mask :BMR.O24 :BMR.H24
acceptor mask :BMR.O26 :BMR.H26

hbond distance 3.5 angle 120.0 out HB_WatD-LipA_BMR.tbl

The hydrogen bonding fraction calculated by adding column \$10 in the table and divide it by 100% and divide it again with number of lipids involved that is 64.

Secondly, I made the lipids as a donor and water as acceptors. The command is shown below:

trajin  \$path/\$system-reimage-set60.traj

###############################
donor mask :1-64.O11,O12,O13,O14,O15,O16,O22,O23,O24,O25,O26

acceptor mask :257-1556.O :257-1556.H1

acceptor mask :257-1556.O :257-1556.H2

hbond distance 3.5 angle 120.0 out HB_LipD-WatA.tbl

The hydrogen bonding fraction calculated by adding column \$10 in the table and divide it by 100% and divide it again with number of lipids involved that is 64.

Is the method for calculating the hydrogen bonding is correct for solvent & solute systems?

For these two calculations I get different values of hydrogen bonding values.

As a final question, how I shall get the total (averaged) hydrogen bonding per lipid?

Many thanks in advance.

Vijay Manickam Achari

(Phd Student )
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Fri Jul 11 2014 - 00:00:03 PDT
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