Hi Shahid,
I encourage you to send MTK++ and MCPB questions to the Amber mailing list. That way, you may receive faster assistance, since several MTK++ developers and knowledgeable users monitor that list. Also, the answers go into a searchable archive that others may benefit from.
My answers follow below.
On 18/4/2011, at 6:12 a.m., M. Shahid wrote:
> I have some confusions about the scripts in the examples of MCPB and from reading the manual.
> I don't understand where can I start from.
There is a wealth of information in the MTK++ manual, $AMBERHOME/doc/MTKpp.pdf. In particular, please refer to section 12 and subsection 15.10, which provides a background to MCPB, as well as instructions (by way of example) concerning its use.
> Should I start from genMetalFF.sh script to create the script files and then follow the NAME.README file
> one by one and provide it manually created NAME_sidechain.bcl and _large.bcl scripts?
Essentially, yes, though in the event of discrepancies between <NAME>.README and the manual, try the instructions in the manual first; I believe it is the more up to date.
> Is it also possible to start from getting _aSite.pdb after using capActiveSite program and then start from running genMetalFF.sh?
I suppose so, though you'll want to make sure your residues are appropriately named, and that the caps are labelled as ACE, NME, etc., rather than being treated as part of the parent. To my knowledge, it hasn't been tested, though. Once again, please see the instruction manual for information on how to use capActiveSite.
> Could you please tell me how should I start and follow the complete workflow?
At this stage, all I could do is repeat what's in the manual. Your best bet would be to start with what you have and contact the mailing list with any questions or problems you have connected with specific steps.
Hope that helps,
Ben
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Received on Mon Apr 18 2011 - 09:00:03 PDT
