Re: [AMBER] cpptraj hbond: query on output

From: George Tzotzos <gtzotzos.me.com>
Date: Thu, 09 Oct 2014 21:00:58 -0300

Thank you Dan

Id be grateful of some additional clarifications.

If I modify the script according to your suggestion (see below) - which I may have misunderstood -

hbond H1 :1-125 :126 nointramol out Nhbond2.agr avgout avg2.dat bridgeout Bridge2.dat solventdonor :WAT solventacceptor :WAT.O

I get a warning: Warning: [hbond] Not all arguments handled: [ :126 ]

and as a consequence no h-bonding interactions of the ligand. Please note :126 is the ligand.

One additional clarification concerning the definition for [UU] (solute-solute bonds). The solute in my case is the receptor-ligand complex. I guess [UU] then refers to receptor-ligand h-bonds. Am I wrong?

Thanks once again for your help

George


On 9Oct, 2014, at 7:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> On Thu, Oct 9, 2014 at 2:33 PM, George Tzotzos <gtzotzos.me.com> wrote:
>> Im trying to work out h-bonds and bridged h-bonds between a ligand and receptor residues ONLY.
>
> If you just want ligand-receptor hbonds You will want to add the
> 'nointramol' keyword to your 'hbond' command so that intra-molecular
> hydrogen bonds are ignored. If you can probably get rid of your
> 'donormask' and 'acceptormask' keywords and let cpptraj search for
> donors and acceptors. What these keywords are doing right now is
> looking for hbond donors in your receptor only and hbond acceptors in
> your ligand only - you really want both acceptors and donors for each.
>
>> I used the following script
>>
>> hbond REC-LIG donormask :1-125 acceptormask :126 out Nhbond.agr avgout REC-LIG.dat bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
>>
>> When I draw (xmgrace) the output Nhbond.agr shows three series REC-LIG[UU], REC-LIG[UV] and REC-LIG[Bridge].
>>
>> The output shows the maximum of per frame interactions to be 2 in the case of REC-LIG[UU] series and 12 in the case of REC-LIG[UV]. The difference between the two datasets is not quite clear to me. Any explanation and/or improvement in the above script would be most helpful.
>
> These are described in the Amber 14 manual in the cpptraj hbond
> command (28.10.24):
>
> [UU] Number of solute-solute hydrogen bonds.
> [UV] Number of solute-solvent hydrogen bonds.
> [Bridge] Number of bridging solvent molecules.
>
> Hope this helps,
>
> -Dan
>
>>
>> Im attaching a graphical output for easy reference
>>
>> Regards
>>
>> George
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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>
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Received on Thu Oct 09 2014 - 17:30:02 PDT
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