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

[Justin Lemkul]

On 6/17/13 4:58 PM, Hyunjin Kim wrote:
> Hi,
>
> 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
> calculation.
>
> 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?
>

Yes.

> 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.
>

The interactions are simply zero.

> 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.
>

There is a similar example in manual section 5.7.4 that may be useful.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================