Re: AMBER: H-bond in ptraj

From: Barbault Florent <florent.barbault.paris7.jussieu.fr>
Date: Fri, 5 Jan 2007 09:20:22 +0100

Hello,

Your problem is in the selection:

> Mask [:4GA.O2] represents 7 atoms
> Mask [:4GA.H20] represents 147 atoms
> WARNING in ptraj, acceptor: There is not a 1-1
> correspondence between the
> atom selection in the two masks :4GA.O2 and :4GA.H20
> which contain 7 and 147
> atoms respectively. Ignoring...

You have to give the correct name selection in order to have a real 1-1
correspondance. It is obvious to do that with proteins and nucleic acids
since the atom names are well defined. I know it is more complicated with
carbohydrates or other organic molecules.
In that last case, you can also put the atom number in selection. It sounds
boring to do that put you will be sure to don't miss any atoms. Here is an
example of how to select atoms:
   acceptor mask :1.O11 @171
    
  Here you have a selection of atom O11 from residue 1 and the atom number 171

Hope this will help you

I wish you a Happy new year


Le vendredi 5 Janvier 2007 05:34, nag raj a écrit :
> Dear Jianyin Shao,
> Thank you for your responce. As per
> your suggestions I defined acceptor, again i am
> getting problem, Here I pasted input as well as out
> put error. Can you tell me how to overcome this
> problem.
> Thank you,
> with regards,
> nagaraju.
> Here is input.
> ####################################################
> trajin b1_lg2_hb_con2_md_run2.crd 1 40 1
>
> prnlev 4
> #
> #Donors & acceptors from beta-cyclodextrine molecule
> #
> donor mask :4GA.O2
> donor mask :4GA.O3
> donor mask :4GA.O4
> donor mask :4GA.O5
> donor mask :4GA.O6
>
> acceptor mask :4GA.O2 :4GA.H20
> acceptor mask :4GA.O3 :4GA.H30
> acceptor mask :4GA.O6 :4GA.H60
>
> prnlev 0
>
> hbond includeself distance 3.6 angle 160 out
> intra_Hbond.out
>
> Here is the out put.
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>
> PTRAJ: acceptor mask :4GA.O2 :4GA.H20
> Mask [:4GA.O2] represents 7 atoms
> Mask [:4GA.H20] represents 147 atoms
> WARNING in ptraj, acceptor: There is not a 1-1
> correspondence between the
> atom selection in the two masks :4GA.O2 and :4GA.H20
> which contain 7 and 147
> atoms respectively. Ignoring...
>
> PTRAJ: acceptor mask :4GA.O3 :4GA.H30
> Mask [:4GA.O3] represents 7 atoms
> Mask [:4GA.H30] represents 0 atoms !!!NO ATOMS
> DETECTED!!!
> WARNING in ptraj, acceptor: No hydrogen atom was
> selected (:4GA.H30), ignoring...
> WARNING in ptraj, acceptor: There is not a 1-1
> correspondence between the
> atom selection in the two masks :4GA.O3 and :4GA.H30
> which contain 7 and 0
> atoms respectively. Ignoring...
>
> PTRAJ: acceptor mask :4GA.O6 :4GA.H60
> Mask [:4GA.O6] represents 7 atoms
> Mask [:4GA.H60] represents 147 atoms
> WARNING in ptraj, acceptor: There is not a 1-1
> correspondence between the
> atom selection in the two masks :4GA.O6 and :4GA.H60
> which contain 7 and 147
> atoms respectively. Ignoring...
>
> PTRAJ: prnlev 0
> PRNLEV: value is now 0
>
> PTRAJ: hbond includeself distance 3.6 angle 160 out
> intra_Hbond.out
> FYI: No output trajectory specified (trajout), none
> will be saved.
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 40 frames.
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (b1_lg2_hb_con2_md_run2.crd) is an AMBER
> trajectory (with box info) with 40 sets
>
> OUTPUT COORDINATE FILE
> NULL entry
>
> ACTIONS
> 1> HBOND output to file intra_Hbond.out,
> data will be sorted, intra-residue interactions
> will be included,
> Distance cutoff is 3.60 angstroms, angle cutoff
> is 160.00 degrees
> Hydrogen bond information will be dumped for
> occupancies > 0.00
> Estimated memory usage for this hbond call:
> 0.00 MB
> donors: 35 acceptors: 0
>
> --- Jianyin Shao <jyshao2004.gmail.com> wrote:
> > It looks to me that no atoms were selected as
> > acceptor. Can you try to use
> > "mask" to define acceptor?
> >
> > Use
> > acceptor mask :4GA.O2 :4GA.H20
> >
> > instead of
> > acceptor 4GA O2 H20
> >
> > This could be a bug in the ptraj, and we will take a
> > look.
> > Thanks for bringing this up and if you can not fix
> > the problem, feel free to
> > let me know.
> >
> > Jianyin
> >
> >
> > On 1/3/07, nag raj <nagaraju_chem.yahoo.co.in>
> >
> > wrote:
> > > Dear Amber users,
> > > I am trying to analyse hydrogen
> > > bonds using ptraj (AMBER8), I am not getting
> >
> > values
> >
> > > any suggestion is appreciated. Here is my ptraj
> > > script file.
> > > # H-bond analysis in cyclodextrine molecule
> > > #
> > > trajin b1_lg2_hb_con2_md_run2.crd 1 40 1
> > >
> > > #-- Donors from beta cyclodextrine
> > > donor mask :1-7.O2
> > > donor mask :1-7.O3
> > > donor mask :1-7.O4
> > > donor mask :1-7.O5
> > > donor mask :1-7.O6
> > >
> > > #-- Acceptors from beta cyclodextrine
> > > acceptor 4GA O2 H20
> > > acceptor 4GA O3 H30
> > > acceptor 4GA O6 H60
> > > hbond distance 3.6 angle 160 print .05 series out
> > > zzzz.out
> > >
> > > Here I attached the out put file,
> > >
> > > 4GA 4GA 4GA 4GA 4GA 4GA 4GA L2H WAT WAT
> > > WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
> > > ...
> > > PTRAJ: donor mask :1-7.O6
> > > Mask [:1-7.O6] represents 7 atoms
> > >
> > > PTRAJ: acceptor 4GA O2 H20
> > >
> > > PTRAJ: acceptor 4GA O3 H30
> > >
> > > PTRAJ: acceptor 4GA O6 H60
> > >
> > >
> > > Processing AMBER trajectory file
> > > b1_lg2_hb_con2_md_run2.crd
> > >
> > > Set 1
> >
> > ........................................
> >
> > > PTRAJ: Successfully read in 40 sets and processed
> >
> > 40
> >
> > > sets.
> > > Dumping accumulated results (if any)
> > >
> > > HBOND SUMMARY:
> > > Data was saved to series out,
> > > data was sorted, intra-residue interactions
> >
> > are
> >
> > > NOT included,
> > > Distance cutoff is 3.60 angstroms, angle
> >
> > cutoff
> >
> > > is 160.00 degrees
> > > Hydrogen bond information dumped for
> >
> > occupancies
> >
> > > > 0.05
> > >
> > > Dumping schematic of time series after each
> >
> > h-bond,
> >
> > > key follows:
> > > | . - o x *
> >
> > .
> >
> > > 0-5% 5-20% 20-40% 40-60% 60-80% 80-95%
> > > 95-100% occupancy
> > >
> > > DONOR ACCEPTORH ACCEPTOR
> > > atom# :res.atom atom# :res.atom atom#
> > >
> > :res.atom
> > :
> > > %occupied distance angle lifetime maxocc
> > >
> > >
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-- 
----------------------------------------------------------
Dr Florent Barbault
Maitre de conferences
Universite Paris VII
Laboratoire ITODYS
1, rue Guy de la Brosse
75005 Paris FRANCE
http://perso.wanadoo.fr/barbault
tel  : (33) 01-44-27-68-21
mail : florent.barbault.paris7.jussieu.fr
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Received on Sun Jan 07 2007 - 06:07:36 PST
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