Dear Prof. Cheatham,
Thank you very much for your help.
As I am interested in the hbond between the drug (DA) and the receptor, but
not the solvent. So, I modify the ptraj file as follows: I was expecting
that it could identify all the H-bond with DA as both donor or acceptor.
==============================================================================
trajin drug_receptor.mdcrd 1 1000
donor DA N1
acceptor DA C2 H2
acceptor DA N6 H61
hbond
==============================================================================
However, no hbond could be found as it is shown here:
==============================================================================
data was sorted, intra-residue interactions are NOT included,
Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information dumped for occupancies > 0.00
DONOR ACCEPTORH ACCEPTOR
atom# :res.atom atom# :res.atom atom# :res.atom %occupied distance
angle
---------------- ---------------------------------
-------------------------------------
==============================================================================
However, when I do the ptraj analysis with the following ptraj file:
==============================================================================
trajin drug_receptor.mdcrd 1 1000
donor DA N1
donor DT3 O2
donor DT3 O4
acceptor DT3 N3 H3
acceptor DA C2 H2
acceptor DA N6 H61
hbond distance 5.0 angle 120.0
=============================================================================
There are several hbonds indentified:
==============================================================================
DONOR ACCEPTORH ACCEPTOR
atom# :res.atom atom# :res.atom atom# :res.atom %occupied distance
angle
| 116 :4.N1 | 24 :1.H3 23 :1.N3 | 100.00 2.760 ( 0.05)
21.84 (11.00)
| 26 :1.O2 | 118 :4.H2 117 :4.C2 | 100.00 3.087 ( 0.08)
40.67 ( 6.83)
| 22 :1.O4 | 114 :4.H61 113 :4.N6 | 100.00 2.928 ( 0.08)
12.32 ( 6.75)
| 26 :1.O2 | 114 :4.H61 113 :4.N6 | 0.40 4.932 ( 0.04)
58.54 ( 1.34)
---------------- ---------------------------------
-------------------------------------
===============================================================================
I was expecting that I could get the same results with both ptraj input
file, however, i was wrong. It seems to me that I need to list out all the
potential hbonding partners of the drug in the ptraj file? Isn't?
One more question regarding hbond is I could like to monitor a
intramolecular hbond WITHIN the drug, can I do it will ptraj commands too?
Best regards and thanks a lot,
Cat
trajin hbond_Topotecan.mdcrd 1 1000
donor DA N1
donor DT3 O2
donor DT3 O4
acceptor DT3 N3 H3
acceptor DA C2 H2
acceptor DA N6 H61
hbond
>From: Thomas Cheatham <tec3.utah.edu>
>Reply-To: amber.scripps.edu
>To: amber.scripps.edu
>Subject: Re: AMBER: hbond ptraj
>Date: Wed, 16 May 2007 21:57:46 -0600 (Mountain Daylight Time)
>
>
> > trajin DNA_drug.mdcrd 1 1000
> > solvent
> > solventdonor DRUG N1
> > solventacceptor DRUG C2 H2
> > solventacceptor DRUG N6 H61
>
>What you want is donor/acceptor, not solventdonor/solventacceptor (those
>are used within the hbond command to allow indistinguishability of
>solvent).
>
>donor DRUG N1
>acceptor DRUG C2 H2
>
>assuming the residue is named "DRUG" which is suspicious since it is a
>4-letter name.
>
> > hbond distance 5.0 angle 120.0
> >
> > However, it comes up with an error message like this:
> >
> > PTRAJ: solventdonor DRUG N1
> > Searching for solvent by residue name DRUG
> > Segmentation fault
>
>What is happening is the "solventdonor" is being interpreted as the
>"solvent" command (which is a way to redefine what is solvent for the
>closest command, among others...).
>
>So, I would do:
>
>donor DRUG N1
>acceptor DRUG C2 H2
>acceptor DRUG N6 H61
>hbond series out hbond.dat distance 5.0 angle 120.0 \
> solventdonor WAT O \
> solventacceptor WAT O H1 \
> solventacceptor WAT O H2
>
>--tec3
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
_________________________________________________________________
Learn English via Shopping Game, FREE!
http://www.linguaphonenet.com/BannerTrack.asp?EMSCode=MSN06-03ETFJ-0211E
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun May 20 2007 - 06:07:17 PDT
