[gmx-users] protein / bilayer problems

[Anton Feenstra]

jxs818 at bham.ac.uk wrote:
> 
> Hi all,
> I am having a bit of trouble putting a protein into a
> bilayer. The first part, actually putting the hole in the
> bilayer went really well (Nice one Graham, for the gromacs
> 3 mdrun_hole version). However, when I merge the bilayer
> and the protein gro files, amend the top file etc and do
> grompp I get the non zero system charge warning (Do I amend
> this through genion???-charge -9.98999 E-01) and the warning
> 
> Warning: atom names in rhod.top and merged.gro don't match
> (N - C1)
> Warning: atom names in rhod.top and merged.gro don't match
> (H1 - C2)
> Warning: atom names in rhod.top and merged.gro don't match
> (H2 - C3)
> Warning: atom names in rhod.top and merged.gro don't match
> (H3 - N4)
> <snip>
> 
> (more than 20 non-matching atom names)
> WARNING 2 [file "rhod.top", line 22458]:
>   12336 non-matching atom names
>   atom names from rhod.top will be used
>   atom names from merged.gro will be ingnored
> 
> I have tried changing the order of .itp files etc in
> the .top file to see if I can get rid of the ?non matching
> atom warnings? but when I do I get the error

It is the order of the entries in the [ molecules ] part of
your .top file, where it says something like:

[ molecules ]
; Compound      #mols
Protein         1
DPPC         1024
SOL         23552

In this case, you must also have the protein first in your .gro file,
then the lipids and then water. 

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
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|  \__/  | "I'd Be Water If I Could" (Red Hot Chili Peppers)         |
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