[gmx-users] g_sdf : error
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Tue May 18 03:20:44 CEST 2010
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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>
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