Re: mm_pbsa

From: samantha hughes <>
Date: Thu 14 Jun 2001 07:06:47 +0000

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
Received on Thu Jun 14 2001 - 00:06:47 PDT
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