AMBER Archive (2007)

Subject: Re: AMBER: H-bond in ptraj

From: nag raj (nagaraju_chem_at_yahoo.co.in)
Date: Thu Jan 04 2007 - 22:34:59 CST


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
> >
> > 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_at_O6
> > Mask [:1-7_at_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_at_atom atom# :res_at_atom atom#
> :res_at_atom
> > %occupied distance angle lifetime maxocc
> >
> >
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