Re: [AMBER] Charmm-gui conversion

From: mohammad r <>
Date: Fri, 11 Dec 2015 05:06:04 +0000 (UTC)

Hi David,
This the commands which I used:> source leaprc.ff14SB> loadAmberParams frcmod.ionsjc_tip3p> mol=loadpdb solvated.pdb
And then I tried to save parameters. CLA is Chloride.By the way, when I save a pdb or parameter files in tleap, it automatically add hydrogen to all the residues. Is there any way to make the tleap not to do that?


    On Friday, December 11, 2015 1:04 AM, David A Case <> wrote:

 On Thu, Dec 10, 2015, mohammad r wrote:

> Created a new atom named: CLA within residue: .R<CLA 13811>
> Creating new UNIT for residue: CLA sequence: 13812

You must load an Amber library for the CLA unit.  I'm assuming you have not
done this, although you fail to mention which libraries you *did* load.

What is CLA? Chloride?  (It appears to be a residue with only a single atom.)
You must make sure that the residue and atom names in the input pdb file match
those in the Amber libraries that you load.  In many cases, this will require
manual editing of the pdb files.

(Note that many uncertainties would be resolved if you posted all of the
commands you gave to tleap, not just the error messages.)


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