[gmx-users] Re: protein in SDS/water

[Mark Abraham]

Thomas Schlesier wrote:
> Hi,
> 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.

Mark