It is most likely due to having the order of your molecules in the topology file (.top) different to those that are in coordinate file (.gro).
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 --------------------------------- 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 kecy...@sina.com Sent: Thursday, 22 April 2010 1:14 PM To: gmx-users@gromacs.org Subject: [gmx-users] warning when process the files with grompp Hello, I want to generate the em.tpr file, but it arise the warning like this : Warning: atom name 1 in TBP_wat.top and 10tbpc12wat1.gro does not match (C13 - OW) Warning: atom name 2 in TBP_wat.top and 10tbpc12wat1.gro does not match (C10 - HW1) Warning: atom name 3 in TBP_wat.top and 10tbpc12wat1.gro does not match (C7 - HW2) Warning: atom name 4 in TBP_wat.top and 10tbpc12wat1.gro does not match (C6 - OW) Warning: atom name 5 in TBP_wat.top and 10tbpc12wat1.gro does not match (O5 - HW1) Warning: atom name 6 in TBP_wat.top and 10tbpc12wat1.gro does not match (P1 - HW2) Warning: atom name 7 in TBP_wat.top and 10tbpc12wat1.gro does not match (O4 - OW) My system is water and dodecane (from 0 to 5 nm of the z axis is water box, 5 to 10 nm dodecane box), and the TBP dissolves in the dodecane, if I overlook it , mdrun can not do the energy minimization well, and the TBP molecule will be tattered. I hope you can help me ,thank you very much!
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