[gmx-users] Distances calculation in umbrella sampling

[Kingsley Theras Primus Dass .]

dear users,
 I am encountering a problem with script, the summary.dat file does
not generate
any value. But if I run the distance command one at the time , it is
generating the value, I could not figure out where I am goingperlgmx wrong.
can anyone tell where lies the mistake?mistake?


Thank you

*below the command line for one distance *
Command line:
  gmx_mpi distance -s sgdp_pull_t.tpr -f conf1.pdb -n index.ndx -oall
dist1.xvgtpr -f conf1.pdb -n index.ndx -oall dist1.xvg -n index. - dist1.xvg
pdbndxoall

Available static index groups:
 Group 0 "System" (89993 atoms)
 Group 1 "Protein" (6541 atoms)
 Group 2 "Protein-H" (5087 atoms)
 Group 3 "C-alpha" (644 atoms)
 Group 4 "Backbone" (1932 atoms)
 Group 5 "MainChain" (2578 atoms)
 Group 6 "MainChain + Cb" (3192 atoms)
 Group 7 "MainChain + H" (3209 atoms)
 Group 8 "SideChain" (3332 atoms)
 Group 9 "SideChain-H" (2509 atoms)
 Group 10 "Prot-Masses" (6541 atoms)
 Group 11 "non-Protein" (83452 atoms)
 Group 12 "Other" (12949 atoms)
 Group 13 "_ *" (19 atoms)
 Group 14 "GDP" (34 atoms)
 Group 15 "POPC" (12896 atoms)
 Group 16 "NA" (107 atoms)
 Group 17 "CL" (106 atoms)
 Group 18 "Water" (70290 atoms)
 Group 19 "SOL" (70290 atoms)
 Group 20 "non-Water" (19703 atoms)
 Group 21 "Ion" (213 atoms)
 Group 22 "_ *" (19 atoms)
 Group 23 "GDP" (34 atoms)
 Group 24 "POPC" (12896 atoms)
 Group 25 "NA" (107 atoms)
 Group 26 "CL" (106 atoms)
 Group 27 "Water_and_ions" (70503 atoms)
 Group 28 "Protein_chain_A" (3536 atoms)
Specify any number of selections for option 'select'
(Position pairs to calculate distances for):
(one per line, <enter> for status / groups, 'help' for help, Ctrl-D to end)

> Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision)
Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision)
Reading frame 0 time 10.000 '', 89993 atoms
Last frame 0 time 10.000
Analyzed 1 frames, last time 0.000
GDP:
  Number of samples: 17
  Average distance: 0.16202 nm
  Standard deviation: 0.05626 nm
Protein_chain_A:
  Number of samples: 1768
  Average distance: 0.19869 nm
  Standard deviation: 0.12505 nm



the error message that I get when I run perl script perl script

readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
Cleaning up ...



2017-11-30 23:10 GMT+08:00 Amir Zeb <zebamir85 at gmail.com>:

> Solved it,
>
> Thanks every one!
>
> Amir
>
> On Thu, Nov 30, 2017 at 5:06 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 11/30/17 4:04 AM, Rose wrote:
> >
> >> Till nowi think the only solution is to use gmx distance for each
> >> conf.gro files.then use perl script.
> >> don't forget to delete gmx distance line from script.
> >>
> >
> > Or run one instance of gmx distance manually to understand how to
> properly
> > use it, diagnose any problems in your selection, etc. and fix the script.
> > There's no reason to reinvent the wheel, just modify the script properly
> to
> > suit your needs.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==================================================
> >
> >
> > --
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