[gmx-users] simulation of a protein including calcium ion

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sat Oct 16 10:39:38 CEST 2010

Dear Leila
Ok,But you have to separate your ions from your general pdb
file(protein+ions) in the form of pdb,
in the other words you need to obtain the pdb files for your ions separately
and then paste it to PRODRG server.because your protein has more than 300
atoms alonly.
I hope it can help you

On Sat, Oct 16, 2010 at 12:00 PM, leila karami <karami.leila1 at gmail.com>wrote:

> Dear mohsen ramezanpour* *
> yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but
> ERRDRG> Too many atoms in this molecule (should be <=300).
> PRODRG> Program terminated unsuccessfully, sorry!
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