On 3/24/13 9:02 AM, Shima Arasteh wrote:
In fact the genion does not add the neutralizing CL ions to gro file! Why?
How can I solve this problem?
Using -nn and -conc is probably incompatible, because -conc will add some number
of ions, which may not play nicely with the fact that you are then manually
saying "add only 3 negative ions" with -nn 3. The correct formation of the
command is to use genion -conc 1 -neutral.
-Justin
Would you please help me?
Sincerely,
Shima
----- Original Message -----
From: Shima Arasteh <shima_arasteh2...@yahoo.com>
To: Discussion list for GROMACS users <gmx-users@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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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