[gmx-users] warning when process the files with grompp

[Dallas B. Warren]

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.warren at 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-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of kecy_wu at sina.com
Sent: Thursday, 22 April 2010 1:14 PM
To: gmx-users at 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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