[gmx-users] g_select error

[Albert]

hello Justin:

   thanks for kind tips.
   I've tried both methods:

g_select -f md.xtc -s npt3.pdb -os size.xvg -sf selection.dat

g_select -f md.xtc -s npt3.pdb -os size.xvg -select 'resname SOL and 
name OW within 0.6 of resid 114'


but they all failed with messages:

--------------------log--------------------

WARNING: masses and atomic (Van der Waals) radii will be determined
          based on residue and atom names. These numbers can deviate
          from the correct mass and radius of the atom type.

selection parser: syntax error
selection parser: invalid selection 'resname SOL and name OW within 0.6 
of resid 114'

-------------------------------------------------------
Program g_select, VERSION 4.5.5
Source code file: trajana.c, line: 1310

Input error or input inconsistency:
selection(s) could not be parsed
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Yeah, a Wuzz, Or a Jerk" (F. Black)






On 11/27/2012 01:54 AM, Justin Lemkul wrote:
>
>
> On 11/26/12 2:08 PM, Albert wrote:
>>
>> hello:
>>
>>   I am going to calculate the number of water molecules within 6 A of
>> residue 114 by following command:
>>
>>
>> g_select -f md.xtc -s npt3.pdb -os size.xvg -select "resid 114 and rdist
>> < 0.6"
>>
>>
>> but it said:
>>
>>
>> WARNING: masses and atomic (Van der Waals) radii will be determined
>>           based on residue and atom names. These numbers can deviate
>>           from the correct mass and radius of the atom type.
>>
>> selection parser: syntax error
>> selection parser: invalid selection 'resid 114 and rdist < 0.6'
>>
>> -------------------------------------------------------
>> Program g_select, VERSION 4.5.5
>> Source code file: trajana.c, line: 1310
>>
>> Input error or input inconsistency:
>> selection(s) could not be parsed
>> For more information and tips for troubleshooting, please check the 
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>
> You haven't defined rdist to actually be anything.  If you need to be 
> using multi-line selections, you should be providing a selection.dat 
> file to -sf instead of using single-line statements to -select.
>
> Something like g_select -select 'resname SOL and name OW within 0.6 of 
> resid 114' should do the trick, but I haven't actually tried that so 
> I'm not 100% sure.
>
> -Justin
>