[gmx-users] g_select problem (Invalid command line argument:)

[Justin A. Lemkul]

leila karami wrote:
> Dear gromacs users
> 
> 
> My system contains protein and water molecules.
> 
> I want to use g_select to obtain residue number of water molecules being 
> within 0.35 nm of protein.
> 
> My index file is as follows:
> 
> [ Protein ]
> 
> [SOL]
> 
> When I use  g_select -f *.xtc -s *.tpr -n index.ndx -oi -select "Close 
> to Protein" resname SOL and within 0.35 of group Protein
> 
> I encountered : 
> 
> Program g_select, VERSION 4.5.1
> Source code file: statutil.c, line: 819
> 
> Invalid command line argument:
> SOL
> 
> Why? How to fix it?

You need to enclose your selection string within ' ' so it is interpreted as a 
single string.  As it stands, the words resname, SOL, and, etc are being 
interpreted as arguments, which they are not.

-Justin

-- 
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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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