You need to work out exactly why you have the mis-match, something is screwy.
Something that you are doing does not add up. What is the charge on the ligand? Appears to be -7. Why when you add 9 Na+ do you then end up with a charge of +8? Seems that you have actually added 17 sodiums from those numbers. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Tuesday, 21 June 2011 12:05 PM To: Discussion list for GROMACS users Subject: [gmx-users] Re: Increase in charge after adding the ligand Hi, Initially while preparing the structure , -2 charge was there on the protein. Next, after adding the ligand and executing grompp statement It showing -9.9 charge. So I added 9 sodium ions. but still its showing +8 charge on the system. what shall I do in this case ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com<mailto:monu46...@yahoo.com>
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