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

[David van der Spoel]

David van der Spoel wrote:
> vijay kumar wrote:
>> what is way to solve this prob Chain identifier '5'
>> was used in two non-sequential blocks (residue 4, atom
>> 4)
> 
oh and since this is not a biomolecule, don use pdb2gmx. search the list.
> 
> 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