(unknown charset) [AMBER] MCPB and sidechain.bcl problem

From: (unknown charset) 高彧辉 <yuhuigao.mail.dlut.edu.cn>
Date: Fri, 22 Aug 2014 20:55:30 +0800 (GMT+08:00)

Hi .all!

I have some difficulties in MCPB.

1st): I edit original my pdb file end run
   MCPB 1234_addHs.bcl -l 1234_addHs.bcl.log
but occurs Error: 1 Error in watProtonate ... exiting
terminate called after throwing an instance of 'MTKpp::MTKException'
Aborted (core dumped)

Then I use tleap to add H

2nd): the 1AMP_OH_sidechain.bcl in tutorial generated manually has no explanation about syntax and meaning in detail,
I don't know how to modify the bcl file precisely for my own system.

Like a sentence:

addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr /NAME/CLR/HD1-1/.ND1 87.0

what does the sentence mean and 87.0 stand for??

I sincerely hope someone can help me!

Thanks
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Received on Fri Aug 22 2014 - 06:00:06 PDT
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