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

From: JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Tue, 13 Dec 2011 14:51:12 +0800

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
3H68_OH_large.com,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 min.in 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.

Best Regards


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

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Received on Tue Dec 13 2011 - 10:30:02 PST
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