On 11/27/12 9:18 AM, Albert wrote:
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
-------------------------------------------------------
Well, like I warned, I wasn't 100% sure of the syntax, so it was no guarantee
that I was right. Reading into the documentation and examples a bit, it seems
that "resname SOL and name OW" should be enclosed within double quotes, within
the single-quoted string. Otherwise, use this selection.dat file:
waterO = name OW;
close = waterO and within 0.6 of resid 114;
close;
It should be possible to do it in one line, but the above set of selections
seems to work fine.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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