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
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
