[gmx-users] Re: protein in SDS/water
Mark.Abraham at anu.edu.au
Wed Jun 17 16:19:42 CEST 2009
Thomas Schlesier wrote:
> i think another problem lies here:
> ; Include water topology
>> #include "spc.itp"
>> ; Include generic topology for ions
>> #include "ions.itp"
>> ; Include topology for SDS
>> #include "SDS.itp"
>> [ system ]
>> ; Name
>> Protein in water with SDS
>> [ molecules ]
>> ; Compound #mols
>> Protein 1
>> SDS 2000
>> SOL 36173
> You have defined your Protein, then the water, then ions and then SDS.
> But in [ molecules ] you have the order Protein - SDS - water; but these
> two orders must be the same.
> -> Delete the line, which Justin suggested und put the *#include
> "SDS.itp"* before the *#include "spc.itp"*, then i think all must be fine.
I believe this is not true. The order within [ molecules ] must match
the ordering in the coordinate file supplied with this .top file to
grompp. There would be no good reason to implement grompp such that it
ignored the molecule type names and required the same ordering of the [
moleculetype ] sections as in [ molecules ] - lookup of string names
would be much more robust and user-friendly.
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