[gmx-users] about grompp

Xu Yong yxuemail at sina.com
Wed Jun 19 08:01:55 CEST 2002

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!

Best Wishes 				

Xu Yong

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