[AMBER] MMPBSA, ligand sequence

From: maghtar <meisam.a63.gmail.com>
Date: Fri, 25 Oct 2013 12:29:28 +0200

Dear AMBER users,
I am new in AMBER. I have a structure including a protein and chromophores.
I want to calculate the vibrational modes of the chromophores. I am
following the AMBER tutorial for the calculation of binding entropy using
MMPBSA; but I am getting the following error:

PrmtopError: Couldn't predict mask from topology files!
Your ligand residues must be sequential in your complex.
There are likely problems with your topology files if this is not the case.
Exiting. All files have been retained.

It seems it is because my ligand is not a protein so the program can not
guess the residues of the ligand. After some search I got to this point
that I need to use the ligand_mask option but I am still getting the same
error. This is my input file:

   endframe=10, keep_files=2,

   nmstartframe=1, nmendframe=10,
   nminterval=1, nmode_igb=1, nmode_istrng=0.1,

All the best,
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Received on Fri Oct 25 2013 - 03:30:03 PDT
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