[gmx-users] Re: Increase in charge after adding the ligand

[Dallas Warren]

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.warren at 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-bounces at gromacs.org [mailto:gmx-users-bounces at 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 ??

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Bharat
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