Re: [gmx-users] adding ions in the genion for multimeric proteins

2014-09-03 Thread rajat desikan 
Hi,

Use genion -neutral and let gromacs do that hard work.

Regards,


On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh ambargrom...@gmail.com
wrote:

 Dear users,

 My protein is a trimer and I want to run md :  on binding of a peptide
 (chain-D) to this trimer (chain-ABC).

 Therefore, I have four chains. So, when I create topol.top file using
 pdb2gmx it automatically divide the topology in four *.itp files:
 topol_Protein_chain_A.itp
 topol_Protein_chain_B.itp
 topol_Protein_chain_C.itp
 topol_Protein_chain_D.itp

 so, in time of running genion command its required to mention the number
 of ions to neutralize the protein.
 Now, each of the protein monomer contains net charge of 2 (qtot) in chain
 A, B and C. D-peptide have final qtot as 0.

 Now the question is : Where can I get final qtot for whole system? Is it
 like that: I have to just sum up all three (2+2+2) and write -nn 6 in
 genion command ? Or the final qtot value is written in somewhere else in
 some file, which I missed?

 I am new to multimeric simulation, any kind of help/lead is much
 appreciated!

 Thanks much
 Sincerely
 Nil
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] adding ions in the genion for multimeric proteins

2014-09-03 Thread Dallas Warren 
When you bundle up the system run file (.tpr), using gmx grompp, to pass to gmx 
genion, it will list in the terminal output the net charge of the entire system.

Additionally, you could simply use the -neutral option and not specify the 
number of ions required, the script will work that out for you. 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 
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