[gmx-users] wat is the way to solve this prob

[David van der Spoel]

vijay kumar wrote:
> what is way to solve this prob Chain identifier '5'
> was used in two non-sequential blocks (residue 4, atom
> 4)


your pdb file is a complete mess. it has fixed format. search internet.
don't use tabs only spaces
> the pdb file is for Si atoms 
> no. of atoms 32 at differeent places
> ATOM  1  Si        .66599000      .66599000     
> .66599000
> ATOM  2  Si      7.30599000      .66599000     
> .66599000
> ATOM  3  Si      5.97401000     2.65401000     
> .66599000
> ATOM  4  Si       .66599000     7.30599000     
> .66599000
> ATOM  5  Si        .66599000     5.97401000    
> 2.65401000
> ATOM  6  Si           .66599000      .66599000    
> 7.30599000
> ATOM  7  Si       2.65401000      .66599000    
> 5.97401000
> ATOM  8  Si       3.98599000     3.98599000    
> 3.98599000
> ATOM  9  Si          2.65401000     2.65401000    
> 2.65401000
> ATOM  10 Si      3.98599000     2.65401000    
> 5.97401000
> ATOM  11 Si      2.65401000     3.98599000     
> .66599000
> ATOM  12 Si      5.97401000     3.98599000    
> 2.65401000
> ATOM  13 Si       .66599000     2.65401000    
> 3.98599000
> ATOM  14 Si      2.65401000     5.97401000    
> 3.98599000
> ATOM  15 Si      3.98599000      .66599000    
> 2.65401000
> ATOM  16 Si      7.30599000     7.30599000     
> .66599000
> ATOM  17 Si     7.30599000     5.97401000    
> 2.65401000
> ATOM  18 Si      3.98599000     5.97401000     
> .66599000
> ATOM  19 Si      7.30599000      .66599000    
> 7.30599000
> ATOM  20 Si      5.97401000      .66599000    
> 3.98599000
> ATOM  21 Si      5.97401000     2.65401000    
> 7.30599000
> ATOM  22 Si      7.30599000     2.65401000    
> 3.98599000
> ATOM  23 Si       .66599000     7.30599000    
> 7.30599000
> ATOM  24 Si      2.65401000     7.30599000    
> 5.97401000
> ATOM  25 Si      .66599000     3.98599000     
> 5.97401000
> ATOM  26 Si     3.98599000     7.30599000     
> 2.65401000
> ATOM  27 Si     2.65401000     3.98599000     
> 7.30599000
> ATOM  28 Si     7.30599000     7.30599000     
> 7.30599000
> ATOM  29 Si     5.97401000     5.97401000     
> 5.97401000
> ATOM  30 Si     5.97401000     7.30599000     
> 3.98599000
> ATOM  31 Si     3.98599000     5.97401000     
> 7.30599000
> ATOM  32 Si     7.30599000     3.98599000     
> 5.97401000
> i need simulation for this at a temp of 300 k
> how to solve the above warning
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se