[gmx-users] question regarding mutation from CH --> COH during free energy calculation

Hyunjin Kim hyunjink at andrew.cmu.edu
Mon Jun 17 22:58:01 CEST 2013


I sent the following email last Saturday and I haven't got any reply yet.
I wonder whether you can suggest something regarding this issue.

Thanks in advance.


I edit my topology file for mutating CH --> COH during free energy

Since one hydrogen atom attached to carbon disappears, while two O and H
atoms are appearing, I build topology file as follows:

    8   opls_169      1    TEST    O       3       -0.7    15.9994
opls_140    0.1      1.008

   13   opls_140      1    TEST   H6       4        0.1      1.008
opls_169   -0.7    15.9994

   18   opls_155      1    TEST   H10      5      0.455      1.008
DUM_155     0.0      1.008

   25   DUM_155       1    TEST   H15      7      0.000      1.008
opls_155  0.455      1.008

My questions are,

1. as you can see, I introduce a dummy atom in the A state and mutate H
--> O and dummy --> H. Is it correct?

2. if it is correct, then how should I build bonded parameters between H
(opls_140) and dummy (opls_155), since they do not exist.

I have searched for mailing list and tutorials, but I am still not clear
what is the correct way to edit topology file for my case.


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