On Mon, Jul 14, 2014 at 2:28 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> 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?
>
Not quite. Assuming that column 10 is the full H-bond occupancy column (I
can't recall the format of this file off the top of my head), this approach
will give you the average number of hydrogen bonds per lipid, but nowhere
in your script have you discriminated between inter- and intra-molecular
hydrogen bonds. So your occupancy values will include intra-molecular
contributions (if any intra-molecular hydrogen bonds satisfy the criteria,
that is).
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?
>
Seems reasonable to me.
> For these two calculations I get different values of hydrogen bonding
> values.
>
Why would you expect them to be the same?
> As a final question, how I shall get the total (averaged) hydrogen bonding
> per lipid?
>
It seems to me that the various hydrogen bond occupancies that you've
computed are additive. i.e., total_hbonds = hbonds_lipid-lipid +
hbonds_lipid-water + hbonds water-lipid. So just add them up.
That said, I highly suggest that you upgrade to AmberTools 14 and switch to
using cpptraj instead. The hbond command has been drastically simplified.
It allows you to specifically omit inter-molecular H-bonds if you want
_without_ having to specify a separate hbond command for each molecule with
a different set of acceptor and donor masks. It also lets you partition
between water-solute and solute-solute hbonds _without_ having to break it
into two steps to avoid counting water-water hbonds. (Also, ptraj adopts
the convention that an "acceptor" is an electron acceptor and a "donor" an
electron donor. cpptraj adopts the convention that an "acceptor" accepts
the hydrogen bond and the "donor" provides the hydrogen, so the meaning of
the two terms is switched in cpptraj compared to ptraj).
The various keywords are described in the Amber 14 manual.
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jul 14 2014 - 09:00:02 PDT
