Re: [AMBER] MTK++ and MCPB patch released

From: Ben Roberts <>
Date: Sat, 24 Dec 2011 11:20:23 -0500

Hi JiYuan,

On 24/12/2011, at 5:58 AM, JiYuan Liu wrote:

> Hi Martin,
> You are great.I have changed the lines of collection.cpp,MCPB is ok now
> but minimization with ligand,the structure of the ligand(CA1) changed so
> worsely as before.
> After wrote parmtop and inpcrd of 3H68_OH_mcpb.pdb,I run "charge
> model",it shown -3.999940

Is a charge of -4.0 what you would expect for this system? The deviation from an integral value is very small and is likely not a problem.

> I also run "charge model.CA1",it shown
> -0.656100,could the charge of CA1 is not zero to be a problem?

Is CA1 a residue or an atom? If an atom, a non-integral partial charge is generally considered OK, though if it's a carbon atom that kind of charge would be considered unusually negative.

> I copied the prep information of CA1 from the 3H68_OH_chg2.prep file,and
> run minimization on the ligand by itself,it's structure still deform.How
> could I solve this problem.

Could you please re-run your minimisation on the ligand itself, reporting energies (in the log file) at every step. Then see which components of the energy term (bond, angle, dihedral, etc.) decrease rapidly, and which ones increase rapidly. This information may provide clues as to which parameters are wrong. Also, save a trajectory at every step, or a restart file at every step, and see how exactly the geometry deforms on a step-by-step basis.


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Received on Sat Dec 24 2011 - 08:30:02 PST
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