[gmx-users] The energy minimization....

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 16 10:27:03 CEST 2007

mjduan at smail.hust.edu.cn wrote:
> http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html
> Mark:
> I am sorry to disturb you. I'm a beginner of GROMACS and this 
> "mailing-list" system. I even don't know how to replay a post directly. 
> And yesterday I haven't seen your replay because the list title changed, 
> sorry again!

To reply to a list email, just reply as you would to any other email.

> About the problem, I haven't resolved it yet. The .top file of my ATP 
> molecule is generated by the pdb2gmx, and the coordinates of each atom 
> adopted to the pdb file. The force file is ffG43a2. Whether my topology 
> file of ATP molecule have something wrong? The topology file of ATP as 
> following:

The .top succeeded in minimizing the solvated structure, so that's a
good start. I think I can see that I was being too subtle for you
earlier with my suggestion that you think about observables that would
tell you whether your topology was working. Have you looked at the
before- and after-minimization structures to see whether they make sense
according to your training at recognizing chemical structures that will
be energy minima? If all of your components look reasonable
post-minimization on their own, and there were no significant warnings
or errors from grompp then your topologies probably are OK too. Then you
should go back and approach your original problem of getting a working
topology for your combination system.


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