[gmx-users] Re: gro does not match top

[Shima Arasteh]

In fact the genion does not add the neutralizing CL ions to gro file! Why?
How can I solve this problem?


 Would you please help me?

Sincerely,
Shima


----- Original Message -----
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Sunday, March 24, 2013 5:16 PM
Subject: gro does not match top



Hi,

I am solving a protein in water. This protein has a charge of +3.
After solvation there is 3272 water molecules.

Next, I use genion command to add NACL 1M and 3 extra CL ions to neutralize the system.
#genion -s ions.tpr -o cyclic_solv_ions.gro -p topol.top -nname CL -nn 3 -conc 1

After this, the top file shows:
 Protein_chain_A     1

SOL         3147
NA               61
CL               61
CL               3

But when I check the cyclic_solv_ions.gro file, there are 60 NA and 60 CL ions! Therefore the top doesnt match with gro file and I get the fatal error.
What' s your suggestions? How does it come? 

Thanks in advance.



Sincerely,
Shima