Hi Quy,
I presume that you have created a schematic diagram of your system (as shown in section 15.10.1). And that you successfully carried out the steps similar to those described in sections 15.10.2- 15.10.5.
The commands below seem correct (without seeing your system it is impossible to be sure).
The copyStdResidue command does exactly as its names implies. That is it takes a regular residue e.g. CYS and makes a new copy. The parameters of this new residue will then be optimized for your system
Hope this helps.
Regards,
Martin.
On 20 Apr 2011, at 17:11, Vo Cam Quy wrote:
> Dear experts
> I am using MCPB to generate the parameters for 2 ZN in a complex with
> protein, one ZN with 3SG of CYS and ND1 of HIS, the later connects to 3SG of
> CYS in 1 protein and 1 SG of CYS in another protein.
> Following the section 15.10 of MTKpp User manual, the
> myProtein_sidechain.bcl is like this, isn't it?
>
> copyStdResidue aminoAcids94/CYS NAME/SG1
> copyStdResidue aminoAcids94/CYS NAME/SG2
> copyStdResidue aminoAcids94/CYS NAME/SG3
> copyStdResidue aminoAcids94/HIE NAME/ND1
> copyStdResidue aminoAcids94/CYS NAME/SG4
> copyStdResidue aminoAcids94/CYS NAME/SG5
> copyStdResidue aminoAcids94/CYS NAME/SG6
> copyStdResidue aminoAcids94/CYS NAME/SG7
> copyStdResidue metals/.ZN NAME/ZN1
> copyStdResidue metals/.ZN NAME/ZN2
>
> Could you please explain me more detail on this file?
> Thank you very much in any advance
> best regards
> Quy
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Received on Wed Apr 20 2011 - 14:30:03 PDT
