Hi Ben,
I used the command "antechamber -i ca.out -fi gout -o ca.prepin -fo
prepi -c resp -s 2 *-nc -2*" to rebuild ca.prepin of my ligand,I used
another command "prep2xml" to build the new calib.xml for my ligand,at
this moment I encountered a new small problem that it represented
excessed symbol 	 in the lines of the new calib.xml.I have attached
the log and output files after performed "prep2xml",Please have a look
for them.
Although I found the small problem in the above,I just delete the symbol
"	" in the calib.xml and replaced the old calib.xml.Everything
looked fine when I performed "sh run.MCPB.csh",I found no difference at
3H68_OH_sidechain_opt.com and 3H68_OH_large_mk.com as before I used the
old wrong calib.xml,so I didn't recalculate the Side Chain Model
Optimization/Frequency Calculation and Large Model Charge
Calculation.Then I performed 5000 steps minimization and 10ps molecule
dynamics,the small molecule,two ZN2+ ions,and the around amino acids
which coordinates two ZN2+ were so stable.I need your help to give me a
judge whether my this solution is reasonable.
Best Regards
JiYuan
于 2011年12月31日 12:02, JiYuan Liu 写道:
> Hi Ben,
>
> I think that I must redo all the procedure of MCPB with the "-nc -2"
> flag set for the ligand,it would take me one or two weeks for the
> gaussian calculation,as soon as I get the results I will tell you at once.
>
> Happy New Year:-)
> JiYuan
>
> 于 2011年12月30日 23:20, Ben Roberts 写道:
>> On 30/12/2011, at 10:12 AM, JiYuan Liu wrote:
>>
>>> Hi Ben,
>>>
>>> When I used the wrong calib.xml to perform the minimization,I have done
>>> your suggestion,the step by step minimization is showed that the one of
>>> the metal ion ZN2+ have a large force to attract the furanic ring oxygen
>>> of the ligand,then the furanic ring was moved right and left until my
>>> ligand was deformed in that position.
>> And which components of the total potential energy are implicated here? The bonds? Angles? Torsions? Something else?
>>
>>
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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
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Received on Wed Jan 04 2012 - 00:30:04 PST
