[gmx-users] g_sdf : error

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Tue May 18 03:31:49 CEST 2010 

As I suspected:

Group    16 (          C2) has   129 elements
Group    17 (          C3) has     1 elements
Group    18 (          C4) has   129 elements

As the error has told you, C3 does not have the same number of elements
as C2 and C4.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Nilesh Dhumal
> Sent: Tuesday, 18 May 2010 11:21 AM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] g_sdf : error
> 
> Here are details.
> the first three groups from GUL residue and the last in cation
> (residue)
> 
> Group     0 (      System) has  2584 elements
> Group     1 (     Protein) has  2456 elements
> Group     2 (   Protein-H) has  1036 elements
> Group     3 (     C-alpha) has     0 elements
> Group     4 (    Backbone) has   128 elements
> Group     5 (   MainChain) has   129 elements
> Group     6 (MainChain+Cb) has   129 elements
> Group     7 ( MainChain+H) has   129 elements
> Group     8 (   SideChain) has  2327 elements
> Group     9 ( SideChain-H) has   907 elements
> Group    10 ( Prot-Masses) has  2456 elements
> Group    11 ( Non-Protein) has   128 elements
> Group    12 (          CL) has   128 elements
> Group    13 (       Other) has   128 elements
> Group    14 (         GUL) has    24 elements
> Group    15 (           O) has     1 elements
> Group    16 (          C2) has   129 elements
> Group    17 (          C3) has     1 elements
> Group    18 (          C4) has   129 elements
> Group    19 (          C5) has     1 elements
> Group    20 (          C6) has   129 elements
> --
> --
> Group    39 (         EMI) has  2432 elements
> Group    40 (           C) has   128 elements
> -
> -
> Group    58 (         H19) has   128 elements
> Group    59 (          CL) has   128 elements
> Group    60 (          CL) has   128 elements
> 
> Select a group: 16
> Selected 16: 'C2'
> Select a group: 17
> Selected 17: 'C3'
> Select a group: 18
> Selected 18: 'C4'
> Select a group: 39
> Selected 39: 'EMI'
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time    0.000
> -------------------------------------------------------
> Program g_sdf, VERSION 4.0.5
> Source code file: gmx_sdf.c, line: 177
> 
> Fatal error:
> For single particle SDF, all reference groupsmust have the same size.
> 
> -------------------------------------------------------
> 
> Nilesh
> 
> 
> On Mon, May 17, 2010 8:23 pm, Dallas B. Warren wrote:
> > Can you copy and paste into here what you see between:
> >
> >
> > "Select a reference group and 1 group"
> >
> >
> > And
> >
> >
> > "Select a group:"
> >
> >
> > When you run the script.
> >
> >
> > Catch ya,
> >
> >
> > Dr. Dallas Warren
> > Drug Delivery, Disposition and Dynamics
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3010
> > dallas.warren at pharm.monash.edu.au +61 3 9903 9167
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to
> resemble
> > a nail.
> >
> >
> >> -----Original Message-----
> >> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >> bounces at gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18
> May
> >> 2010 9:29 AM
> >> To: Discussion list for GROMACS users
> >> Subject: RE: [gmx-users] g_sdf : error
> >>
> >>
> >> hey Sorry for typing mistake.
> >> I used ths command.
> >> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt
> -r
> >>
> >> Nilesh
> >>
> >>
> >> On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote:
> >>
> >>>> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o
> sdf.plt
> >>>>
> >> -r
> >>
> >>>
> >>> Is that the exact command line you used?  If so, doubt it would
> >>>
> >> actually
> >>> work, since it should be:
> >>>
> >>> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o
sdf.plt
> > -
> >
> >> r
> >>>
> >>> Catch ya,
> >>>
> >>>
> >>>
> >>> Dr. Dallas Warren
> >>> Drug Delivery, Disposition and Dynamics
> >>> Monash Institute of Pharmaceutical Sciences, Monash University
> >>> 381 Royal Parade, Parkville VIC 3010
> >>> dallas.warren at pharm.monash.edu.au +61 3 9903 9167
> >>> ---------------------------------
> >>> When the only tool you own is a hammer, every problem begins to
> >>>
> >> resemble
> >>> a nail.
> >>>
> >>>> -----Original Message-----
> >>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> >>>> bounces at gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, 18
> >> May
> >>
> >>>> 2010 5:55 AM
> >>>> To: gmx-users at gromacs.org
> >>>> Subject: [gmx-users] g_sdf : error
> >>>>
> >>>>
> >>>>
> >>>> Hello,
> >>>> I am trying to run g_sdf for sovlation for glucose in ionic
> >>>>
> > liquids.
> >>>> I am trying to find distribution of anion around glucose.
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o
> sdf.plt
> >>>>
> >> -r
> >>
> >>>>
> >>>> First three group I selected from the same residue (Glucose).
> Forth
> >>>>  grouup I selected from as anion (Anion residue ). I am geting
> >> following
> >>>>
> >>> error.
> >>>>
> >>>> Fatal error:
> >>>> For single particle SDF, all reference groupsmust have the same
> >>>>
> >> size.
> >>>>
> >>>>
> >>>> Thanks
> >>>>
> >>>>
> >>>>
> >>>> Nilesh
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> --
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Use
> >> the
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