[gmx-users] genion

[Dmitry Kovalsky]

Hi there
I'm trying to insert 1 Na+ into a system but what in speial way. I want to 
replace water not from general solvent group but replace some watrer molecule 
around certain residue. So I have created an additional group in index.ndx 
file where 8 water molecules were defined. And when I make  in little are
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genion -s 1Na.tpr -o Na1.gro -np 1 -pname NA+ -n index.ndx
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and while processing genion I'm selecting group 15
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WARNING: turning of free energy, will use lambda=0
Reading file genion_1Na.tpr, VERSION 3.1.3 (single precision)
Reading file genion_1Na.tpr, VERSION 3.1.3 (single precision)
Using a coulomb cut-off of 1.4 nm
Select a continuous group of solvent molecules
Group     0 (      System) has 23857 elements
Group     1 (     Protein) has  1896 elements
Group     2 (   Protein-H) has  1516 elements
Group     3 (     C-alpha) has   198 elements
Group     4 (    Backbone) has   594 elements
Group     5 (   MainChain) has   794 elements
Group     6 (MainChain+Cb) has   966 elements
Group     7 ( MainChain+H) has   984 elements
Group     8 (   SideChain) has   912 elements
Group     9 ( SideChain-H) has   722 elements
Group    10 ( Prot-Masses) has  1896 elements
Group    11 ( Non-Protein) has 21961 elements
Group    12 (         SOL) has 21957 elements
Group    13 (         CL-) has     4 elements
Group    14 (       Other) has 21961 elements
Group    15 (      around) has    21 elements
Select a group: 15
Fatal error: The solvent group is not continuous: index[3]=9381, index[4]=9364
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What  does this mean? 


Sincerely yours,

Dima

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589