[gmx-users] Ligand breaks during energy minimization

Soumya Lipsa Rath soumyalipsabt at gmail.com
Sat Mar 26 06:52:06 CET 2016

>> Dear Justin and Nikhil,
>> Many thanks for your suggestions. Justin, I had optimized the parameters
>> using VMD's FFTK toolkit, so I just replaced my results in the *.str file
>> obtained from paramchem.
>> I tried minimizing the ligand in vaccum and in a solvent box, in both
>> cases, the molecule just scatters apart (pardon me, the bond doesn't
>> break).
>> I think there might be something wrong with the topology. However, I just
>> followed the general steps.

>Well, when relying on automated methods fails, you have to roll your
sleeves up
>and do the work yourself :)
>If you can provide the stream file and coordinates of the ligand, I will
try to
>offer suggestions; if you can share them publicly across the list it may be
>informative for others to listen in on the conversation.
>Note, though, that the CGenFF paper is itself a tutorial on how to
>small molecules, and there are even more detailed CGenFF tutorials
>online (check our website).

Dear Justin,

I could solve the problem finally! It was a stupid error where the input
str file had problems in the angle definition. Now, I rechecked each of the
steps and found the mistake.

Thank you once again for all your suggestions.


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