Hi,
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
JiYuan
于 2011年12月29日 00:25, Jacopo Sgrignani 写道:
> Dear Jiyuan
> MCPB is reasonable, the second method in my opinion is very
> unsatisfactory (and wrong), actually it does not conserve the X-ray
> structure.
> There are a lot of literature about metalloproteins simulations maybe
> you can read L.Banci Curr Opin Chem Biol. 2003 Feb;7(1):143-9.
>
> But the are also other interesting, and more recent review. However
> also in this work of the 2003 there are some still valid lessons to
> simulate metallo-proteins.
>
> Jacopo
>
>
> 2011/12/28 JiYuan Liu<liujiyuan.nwsuaf.edu.cn>:
>> Hi everyone,
>>
>> 3H68 is a metalloprotein that includes two ZN2+/MN2+,the ligand which is
>> a small molecule has dicarboxylic acid that be in ionization state in
>> the metal center.Metal M1 is coordinated by three ligand oxygens (by one
>> oxygen from each carboxylate moiety and by the furanic ring oxygen),
>> while metal M2 is coordinated by only one of the carboxylate oxygens,
>> which is bridging with M1.Now I used two methods to handle this
>> metalloprotein named 3H68,who could tell me which method is reasonable:
>>
>> 1. I used MCPB to handle the metal center includes the ligand of 3H68.
>>
>> 2. I only consider the Electrostatic and VDW in 3H68,the ligand is given
>> the RESP charge with it's value -2,two ZN2+ is used 2+ for it's
>> charge,and the protein used the GAFF,I have run 1 ns MD for 3H68 with
>> second method to solve the metal center included ligand,the result is
>> that two Zn2+ and ligand were so stable in the metal center,but the pose
>> of the ligand with metal center is changed worsely compare to the
>> crystal structure.
>>
>> Best Regards
>> JiYuan
>>
>> --
>> 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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
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 Thu Dec 29 2011 - 05:30:03 PST
