AMBER Archive (2007)

Subject: Re: AMBER: H-bond in ptraj

From: nag raj (nagaraju_chem_at_yahoo.co.in)
Date: Sat Jan 06 2007 - 01:22:10 CST

Dear Barbault Florent,
                     Thank you very much. I fallowed
your suggestion it is working fine. One more doubt is
that how to calculate the total occupency of the
system. I don't want to concentrate on individual
atoms occupiencies. I need overall occupency of the
system.
Example, if i have 100 conformations, in how many
conformations hydrogen bond is existing? I hope that
my problem is understood to you. Thank you very much
for your wishes and WISHING YOU VERY HAPPY NEW YEAR.
                  Thank you.
                                          with
redards,
                                          Nagaraju.
--- Barbault Florent
<florent.barbault_at_paris7.jussieu.fr> wrote:

> Hello,
>
> Your problem is in the selection:
>
> > Mask [:4GA_at_O2] represents 7 atoms
> > Mask [:4GA_at_H20] represents 147 atoms
> > WARNING in ptraj, acceptor: There is not a 1-1
> > correspondence between the
> > atom selection in the two masks :4GA_at_O2 and
> :4GA_at_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_at_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_at_O2
> > donor mask :4GA_at_O3
> > donor mask :4GA_at_O4
> > donor mask :4GA_at_O5
> > donor mask :4GA_at_O6
> >
> > acceptor mask :4GA_at_O2 :4GA_at_H20
> > acceptor mask :4GA_at_O3 :4GA_at_H30
> > acceptor mask :4GA_at_O6 :4GA_at_H60
> >
> > prnlev 0
> >
> > hbond includeself distance 3.6 angle 160 out
> > intra_Hbond.out
> >
> > Here is the out put.
> >
>
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> >
> > PTRAJ: acceptor mask :4GA_at_O2 :4GA_at_H20
> > Mask [:4GA_at_O2] represents 7 atoms
> > Mask [:4GA_at_H20] represents 147 atoms
> > WARNING in ptraj, acceptor: There is not a 1-1
> > correspondence between the
> > atom selection in the two masks :4GA_at_O2 and
> :4GA_at_H20
> > which contain 7 and 147
> > atoms respectively. Ignoring...
> >
> > PTRAJ: acceptor mask :4GA_at_O3 :4GA_at_H30
> > Mask [:4GA_at_O3] represents 7 atoms
> > Mask [:4GA_at_H30] represents 0 atoms !!!NO ATOMS
> > DETECTED!!!
> > WARNING in ptraj, acceptor: No hydrogen atom was
> > selected (:4GA_at_H30), ignoring...
> > WARNING in ptraj, acceptor: There is not a 1-1
> > correspondence between the
> > atom selection in the two masks :4GA_at_O3 and
> :4GA_at_H30
> > which contain 7 and 0
> > atoms respectively. Ignoring...
> >
> > PTRAJ: acceptor mask :4GA_at_O6 :4GA_at_H60
> > Mask [:4GA_at_O6] represents 7 atoms
> > Mask [:4GA_at_H60] represents 147 atoms
> > WARNING in ptraj, acceptor: There is not a 1-1
> > correspondence between the
> > atom selection in the two masks :4GA_at_O6 and
> :4GA_at_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_at_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_at_O2 :4GA_at_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_at_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_at_O2
> > > > donor mask :1-7_at_O3
> > > > donor mask :1-7_at_O4
> > > > donor mask :1-7_at_O5
> > > > donor mask :1-7_at_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
> > > >
>
=== message truncated ===

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