Re: [AMBER] problem with reduce and energy minimization

From: Maryam Hamzehee <>
Date: Sun, 24 Jan 2016 09:59:04 +0000 (UTC)

Dear Prof. Case
Many thanks for your valuable comment, I first did the energy minimization for the ligand and prepared the new complex (ligand-receptor). The problem was fixed successfully.  
Best regardsMaryam

    On Thursday, 21 January 2016, 16:24, David A Case <> wrote:

 On Thu, Jan 21, 2016, Maryam Hamzehee wrote:
> I am trying to do energy minimization of my ligand-protein complex. My
> ligand is small molecule. I followed the tutorial Antechamber tutorial
> (Simulating Sustiva (efavirenz)-RT complex). I did not manage to add
> hydrogens to the ligand (extracted from crystal structure). I used
> reduce command and got the following error:

> Res "LZU" not in HETATM
> Connection Database. Hydrogens not added.

Correct: reduce only adds hydrogens for residue that it has in its database.
> I added hydrogens to the ligand through GOLD software and removed the
> connections from the corresponding file. I continued the procedure
> without using reduce command, and produced the *.frcmod and *.lib
> files. But when I was trying to do energy minimization via sander
> command it stopped suddenly :

Have you minimized the ligand by itself?  From your min.out file, it looks
like you have two atoms on top of each other.  You can use the checkoverlap
command in cpptraj (or maybe the checkValidity command in parmed) to look for
bad atom-atom contacts.  Your ligand looks fine to me, and I don't see
anything obviously wrong (quick look!) in the complex.pdb file.  This is why
the computerized checks are very helpful.

...good luck...dac

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