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

leila karami karami.leila1 at gmail.com
Tue Nov 30 12:50:22 CET 2010

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
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;

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?
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
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