[gmx-users] about grompp

[Anton Feenstra]

Xu Yong wrote:
> 
> Hi, everyone
> 
> I have taken  the coordinate of popc.pdb (128popc+2460h2o) from Tieleman's website. I want to put my membrane protein into it, so I dig a hole in the popc.pdb and get hole.pdb. When I do grompp, the machine give this information:
>            Fatal error: number of coordinates in coordinate file (all.gro, 17136)
>                         does not match topology (all.top, 15993)
> before do grompp, I have done that;
> 
> cat myprotein.pdb hole.pdb >all.pdb
> 
> pdb2gmx -f myprotein.pdb -o myprotein.gro -p myprotein.top -ignh
> 
> vi myprotein.top and added
> # include "lipid.itp"
> # include "popc.itp' and
> popc    75
> sol   2393
> and rename it as all.pdb
> 
> editconf -f all.pdb -o all.gro
> 
> grompp -f em.mdp -c all.gro -p all.top  -o all.tpr
> 
> I didn't know what is the difference of this two number and how to solve this problem.
> Thanks for any help in advance!

This has to do with the number of 'popc' and 'sol' molecules that you 
specify in myprotein.top. There are three things to consider: 1) pdb2gmx
might add hydrogen atoms to your protein, so myprotein.pdb might contain
less atoms than myprotein.gro; 2) the number of popc (75) and sol (2393) 
molecules that you specify in your .top file must correspond to the 
number of these molecules in your 'hole.pdb' (or 'all.pdb', should be 
equal) file; 3) there may be crystal waters in myprotein.pdb, which 
must be added to the number of sol molecules.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
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