Hi, Pengfei!
Thanks a lot for your help!
But i didn't receive any attachment.
Could you send again or paste it??
Best!
> -----原始邮件-----
> 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
> 发送时间: 2014年8月27日 星期三
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] MCPB and sidechain.bcl problem
>
> Hi Yuhui,
>
> I checked the input file. You could not choose the backbone oxygen is because you did not
> include the backbone in the sidechain model. : ) It is the normal situation that you don't
> need to consider the backbone atoms, but since there are backbone atoms coordinated to the metal
> ion, you need to consider it apparently.
>
> I have changed the input file a little bit. Take the backbone of VAL and TRP into consideration.
> Then I used the CH3 group to capped the backbone in two directions.
>
> I used the 2xjp_fixed_H.pdb file directly, so there is some residue number changes in the input file.
>
> Here is the input file after modification.
>
>
>
>
> Meanwhile, you can try the nonbonded model to simulate the Ca2+ ion since there is usually not very strong
> coordinated bond between the Ca ion and the surrounding residues.
>
> You can check the following paper if interested.
> http://pubs.acs.org/doi/abs/10.1021/ct400146w
>
> Hope it helps,
>
> Pengfei
>
> On Aug 25, 2014, at 11:32 PM, Chris Gao <yuhuigao.mail.dlut.edu.cn> wrote:
>
> > Thank you for your help, Pengfei!
> >
> > I send a .tar file containing my pdb file, bcl file and README with detail information about my protein and my question!
> >
> >
> > I hope this do not bother to you！
> >
> > Best,
> > Gao
> >
> >> -----原始邮件-----
> >> 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
> >> 发送时间: 2014年8月25日 星期一
> >> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> >> 抄送:
> >> 主题: Re: [AMBER] MCPB and sidechain.bcl problem
> >>
> >> Hi Yuhui,
> >>
> >> It seems that this is because of the naming of the atoms in the residue. Can you send me the input files
> >> for this step? I can help to check them.
> >>
> >> All the best,
> >> Pengfei
> >>
> >> On Aug 24, 2014, at 7:21 AM, Chris Gao <yuhuigao.mail.dlut.edu.cn> wrote:
> >>
> >>> Thanks, Pengfei!
> >>>
> >>> I now successfully modify the sidechain.bcl file for my system but new questions come that:
> >>>
> >>> The metal Calcium in my protein's active site links with .O.. atom which is not on sidechain
> >>>
> >>> so, The sidechain.bcl is that:
> >>>
> >>> # Create bonds with Calcium
> >>> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/AN1/.OD1
> >>> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/VA1/.O.. (VA1=VAL)
> >>> createBond /NAME/CLR/CA1/C0.. /NAME/CLR/TR1/.O.. (TR1=TRP)
> >>>
> >>> that first line OD1 has no problem, but the last two containg .O.. atom in backbone. I check the bcl.log file, it says:
> >>>
> >>> ### ### ### ###
> >>> ### MTK++ Info ###
> >>> ### Function: selection::parse ###
> >>> ### Message: selection string = /2xjp/CLR/VA1/.O..
> >>> ### ### ### ###
> >>>
> >>> ### ### ### ###
> >>> ### MTK++ Error ###
> >>> ### Function: selection::parse ###
> >>> ### Message: /col/mol/smol/atom selection error (7) ... exiting
> >>> ### ### ### ###
> >>>
> >>> ### ### ### ###
> >>> ### MTK++ Error ###
> >>> ### Function: MCPB::createBond ###
> >>> ### Message: Error in selection parsing ... exiting
> >>> ### ### ### ###
> >>>
> >>> It seems that sidechain.bcl only pocess metal interacts with sidechain??? Not atom in backbone??
> >>>
> >>>
> >>> Thanks for your kind help!
> >>>
> >>> Yuhui
> >>>
> >>>
> >>>
> >>>> -----原始邮件-----
> >>>> 发件人: "Pengfei Li" <ambermailpengfei.gmail.com>
> >>>> 发送时间: 2014年8月23日 星期六
> >>>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> >>>> 抄送:
> >>>> 主题: Re: [AMBER] MCPB and sidechain.bcl problem
> >>>>
> >>>> Hi Yuhui,
> >>>>
> >>>> On Aug 22, 2014, at 8:55 AM, 高彧辉 <yuhuigao.mail.dlut.edu.cn> 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,
> >>>> Pengfei
> >>>>
> >>>>> _______________________________________________
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> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
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> >>
> >>
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Received on Tue Aug 26 2014 - 23:00:02 PDT
