Hi Leila
> 1- where can I found exactly the md5_crd1.Z to run the script in the
> src/mm_pbsa directory?
I asked the same question myself about a year ago- it does not
seem to be available.
> 2-I want tocompute the binding free energy using only the trajectory of
> the complex. Do we need to define the anal_ligand and the anal_receptor
> input ?
No, but change the $suffix variable to just be $SUFFIX_C
> 3- In this case (calculating the binding free energy using only the
> trajecotry of the complex) the RSTART and the RSTOP should they be
> defined or not?
Yes, I dont think it will work otherwise. Anyhow,you usually need
these keywords if have waters/counterions present in your system,
as you dont want to include them in your mm pbsa calculations
Hope this helps
Samantha
Received on Thu Jun 14 2001 - 00:06:47 PDT
