[gmx-users] g_sdf : error
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Tue May 18 03:58:41 CEST 2010
Thanks. Its working.
Why all coordinates are zero in refmol.gro file.
NIlesh
On Mon, May 17, 2010 9:31 pm, Dallas B. Warren wrote:
> 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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>>>>>>
>>>>>>
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