Re: [AMBER] The charge is wrong when the ligand together with the large model in MCPB

From: Ben Roberts <>
Date: Wed, 14 Dec 2011 15:48:38 -0500

Hi JiYuan,

On 13/12/2011, at 1:51 a.m., JiYuan Liu wrote:

> Hi Ben,
> I added my ligand(a small molecule) in the side chain model and large
> model,after I runned the BCL script 3H68_OH_large.bcl,I can get
>,so I used gaussian to optimize it with the parameters
> #N B3LYP/6-31G*
> integral(Grid=UltraFine) pop(mk,readradii) scf=xqc iop(6/33=2) ,it can
> be normal termination,then I can use the script run.mcpb.csh to get the
> prep and frcmod files.When I runed the with the parmtop that be
> generated by MCPB,the two ZN
> ions is stable after the minimization,but the ligand is deformed very
> serious.I suspected that it can not generate the right charge if add a
> small molecule in the large moldel.I tried to change the charge of the
> atom C2 C3 H6 with the small
> molecule CA1 in the prep file,it could be tended to normal after
> minimization.I have attached the files to you,please help me,I have
> taken two weeks to solve it,but not get the right results.Thank you.

OK, we'll take a look at it and see what we find.


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Received on Wed Dec 14 2011 - 13:00:02 PST
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