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

From: JiYuan Liu <>
Date: Wed, 28 Dec 2011 12:35:15 +0800

Hi Martin,

I found a problem with my ligand for it's charge,because my ligand
includes dicarboxylic acid,so it' charge could be -2.But when I added my
ligand to MCPB,I used the command "antechamber -i ca.pdb -fi pdb -o
ca.prepin -fo prepi -c bcc -s 2" and "parmchk -i ca.prepin -f prepi -o
ca.frcmod" to get the files ca.frcmod and ca.prepin,I forgot to add "-nc
-2" to the first command,then I used frcmod2xml,prep2xml to convert
ca.frcmod,ca.prepin,so I got the wrong calib.xml.
My question is that if I used this wrong calib.xml in MCPB,could it only
affect the partial charges for metal center?The force constants of metal
center is affected too?

Best Regards

于 2011年12月25日 00:20, Ben Roberts 写道:
> 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.
> Regards,
> Ben
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Jiyuan Liu
Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
Northwest A&F University
Yangling, Shaanxi
China 712100
Phone: 86-29-87092190
AMBER mailing list
Received on Tue Dec 27 2011 - 21:00:03 PST
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