Re: [AMBER] MCPB and sidechain.bcl problem

From: Pengfei Li <>
Date: Sat, 23 Aug 2014 08:34:24 -0400

Hi Yuhui,

On Aug 22, 2014, at 8:55 AM, 高彧辉 <> wrote:

> 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

That is right. MCPB may met problem when adding the hydrogens on water. Other tools could be used at this situation.

> 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??

In this example we used the methyl group to replace the CA atom in the backbone.
87.0 is the dihedral values between the CA, CB, CG and ND1 atoms of that residue in the original PDB file.
(If you met a negative dihedral value in PDB, you need to change it to positive by adding 360 degree in the MCPB script.)
The dihedral values may be different for different residues, you need to check them manually before setting them in the script.

> I sincerely hope someone can help me!

Sorry for that there is no notes for that part, I will add notes in that part in the corresponding file in that tutorial.

> Thanks

No problem.

All the best,

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Received on Sat Aug 23 2014 - 06:00:02 PDT
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