[AMBER] free energy calculation

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Thu, 26 Sep 2019 15:25:56 +0100

Dear Amber users
I am writing this email again in hope to get a reply on a problem which I
am facing regarding free energy calculation. From mailing list earlier I
asked about free energy calculation tutorial and I could not get reply.
Could you please guide me a little as I am running this calculation first
time and I am greatly confused the way tutorial works.
I am following this tutorial
http://ambermd.org/tutorials/advanced/tutorial9/#overview to calculate the
relative free energy of ligand with the complex.
There are many problems in running this tutorial.
1. It doesn't generate parameters at the first stage as mentioned in the
script 1_leap.sh however if I change force field to leaprc.protein.ff14SB
it works.
2. In the tutorial, it is mentioned just to run script 2_run_md.sh after
1_leap.sh however it doesn't submit any job unless I run run_all_md.sh
script in each complex prepare and ligand prepare directory respectively.
3. When I am doing un_all_md.sh script in for complex directory it is
giving following error:-
| ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
 Input errors occurred. Terminating execution.
which indicates that some box information is missing.
I have followed the script for box information. Where I am doing wrong?

Could you please guide me what actually I should do as running 2_run_md.sh
in the base directory doesn't work. Do I need to run a separate MD for both
ligand and complex in the setup process? if yes then to run 2_run_md.sh in
the base directory.

Hoping to get a reply from experts.

Thank you


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Received on Thu Sep 26 2019 - 07:30:04 PDT
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