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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Received on Sun Jan 07 2007 - 06:07:33 PST
