For anyone to have a chance to help you, you are going to have to provide more details than simply stating "blew up".
What command line did you use, actually paste it in here? What molecule / protein? What forcefield? Paste the actual output from the command in here, showing exactly what you mean by "blew up". Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of Hao Sun Sent: Monday, 26 July 2010 12:36 PM To: [email protected] Subject: [gmx-users] hydrogen-bonded complex Dear all, I am trying to simulate a hydrogen-bonded complex. When I treated the pdb file with pdb2gmx, the structure of gro file blew up. Could you give me some hint on what the potential problem is? What and in which file should I give some specification for hydrogen bonding? Many thanks. With best regards. Yours sincerely, Hao Sun
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