[gmx-users] g_select / Input error or input inconsistency

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 30 13:12:43 CET 2010

leila karami wrote:
> Dear Teemu Murtola
> I study interaction of protein-dna in water. I want to obtain number of 
> water molecule which are simultaneously closer than 3 A° from protein  
> and DNA.
> my selection.dat file is as follows:
> waterO = group SOL and name OW;
> heavy1 = group Protein and group "Protein-H";
> heavy2 = group DNA and group "Protein-H";
> inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2;
> inter;
> when I use g-select -f .xtc -s .tpr -n .ndx -sf ,
> selection parser: syntax error
>  heavy1 = group Protein and group "Protein-H"'
> -------------------------------------------------------
> Program g_select, VERSION 4.5.1
> 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
> Am I doing it incorrect ?  Is there problem in my .ndx file?

I have never used g_select, but it seems to me there could be several problems. 
  The group heavy1 is redundant - atoms that are in "Protein" and "Protein-H" 
will, by necessity, just be "Protein-H."  Perhaps the parser is complaining 
about the inconsistency in the lines - sometimes you have a group name enclosed 
in quotes and sometimes you do not.

I doubt that heavy2 can be satisfied - how can an atom be in both "DNA" and 
"Protein-H" simultaneously?  I think what you might want there is an "or" 
instead of "and."  You probably don't want a merged Protein-H/DNA group anyway, 
because then in your last line you are identifying any water O atom within 0.3 
nm of any Protein-H or DNA atom, not those that are specifically between the two.


> Is this error a bug in gromacs 4.5.1?
> ----
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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