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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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