HI Yuhui,
Maybe there is some problems or tricks about the mailist I don't know…
Just to make sure you can receive it, here I paste the content of the file in the mail.
Hope it helps!
Pengfei
>>2xjp_sidechain.bcl
# Load settings
source 2xjp_settings.bcl
# Create non-standard residue library
createStdGroup NAME
copyStdResidue aminoAcids94/ASP NAME/AS1
copyStdResidue aminoAcids94/ASP NAME/AS2
copyStdResidue aminoAcids94/ASN NAME/AN1
copyStdResidue aminoAcids94/VAL NAME/VA1
copyStdResidue aminoAcids94/TRP NAME/TR1
copyStdResidue metals/.CA NAME/CA1
# Create new atom types
copyAtomType parm94/O2 NAME/OA
copyAtomType parm94/O2 NAME/OB
copyAtomType parm94/O2 NAME/OC
copyAtomType parm94/O2 NAME/OD
copyAtomType parm94/O2 NAME/OE
setAtomType NAME/AS1/.OD2 NAME/OA
setAtomType NAME/AS2/.OD2 NAME/OB
setAtomType NAME/AN1/.OD1 NAME/OC
setAtomType NAME/AN1/.O.. NAME/OD
setAtomType NAME/AN1/.O.. NAME/OE
# write standard library
writeLib NAME NAME.xml
# Open PDB file
readPdb NAME NAME_fixed_H.pdb
# Assign S-S bonds
assignDisulfideBonds
# Atom type
atomType
# Assign bonds, angles, and torsions
assignConnectivity
# Add hydrogens
#addHs /NAME/
#################### CLUSTER ####################
# Create molecule named CLR
createMolecule CLR
# Create HD1-1
createResidue AS1 in CLR
addToResidue /NAME/CLR/AS1 /NAME/1/ASP-147 not bb
# Create AS2-2 from ASP-179
createResidue AS2 in CLR
addToResidue /NAME/CLR/AS2 /NAME/1/ASP-148 not bb
# Create AS1-3 from ASP-117
createResidue AN1 in CLR
addToResidue /NAME/CLR/AN1 /NAME/1/ASN-211 not bb
# Create GL1-4 from GLU-152
createResidue VA1 in CLR
addToResidue /NAME/CLR/VA1 /NAME/1/VAL-213
# Create HD2-5 from HID-256
createResidue TR1 in CLR
addToResidue /NAME/CLR/TR1 /NAME/1/TRP-215
# Create ZN1-6 from ZN-501
createResidue CA1 in CLR
addToResidue /NAME/CLR/CA1 /NAME/2/.CA-259/C0..
addFragment terminal/CH3 bd /NAME/CLR/AS1-1/.CB. ag /NAME/CLR/AS1-1/.CG. tr /NAME/CLR/AS1-1/.OD2 343.2
addFragment terminal/CH3 bd /NAME/CLR/AS2-2/.CB. ag /NAME/CLR/AS2-2/.CG. tr /NAME/CLR/AS2-2/.OD2 111.1
addFragment terminal/CH3 bd /NAME/CLR/AN1-3/.CB. ag /NAME/CLR/AN1-3/.CG. tr /NAME/CLR/AN1-3/.OD1 16.5
addFragment terminal/CH3 bd /NAME/CLR/VA1-4/.C.. ag /NAME/CLR/VA1-4/.CA. tr /NAME/CLR/VA1-4/.N.. 150.6
addFragment terminal/CH3 bd /NAME/CLR/VA1-4/.N.. ag /NAME/CLR/VA1-4/.CA. tr /NAME/CLR/VA1-4/.C.. 296.7
addFragment terminal/CH3 bd /NAME/CLR/TR1-5/.C.. ag /NAME/CLR/TR1-5/.CA. tr /NAME/CLR/TR1-5/.N.. 151.7
addFragment terminal/CH3 bd /NAME/CLR/TR1-5/.N.. ag /NAME/CLR/TR1-5/.CA. tr /NAME/CLR/TR1-5/.C.. 203.4
# Create bonds with zinc1
createBond /NAME/CLR/CA1/C0.. /NAME/CLR/AS1/.OD2
createBond /NAME/CLR/CA1/C0.. /NAME/CLR/AS2/.OD2
createBond /NAME/CLR/CA1/C0.. /NAME/CLR/AN1/.OD1
createBond /NAME/CLR/CA1/C0.. /NAME/CLR/VA1/.O..
createBond /NAME/CLR/CA1/C0.. /NAME/CLR/TR1/.O..
# Atomtype
atomType /NAME/CLR
# Assign bonds and angles
assignParameters /NAME/CLR
# Add Bond and Angle Parameters
addBondAndAngleParameters /NAME/CLR NAME
# Write FRCMOD file
writeParams NAME NAME_params.xml
# Write pdb/mol files
writePdb /NAME/CLR NAME_sidechain.pdb
writeMol /NAME/CLR NAME_sidechain.mol
writeSdf /NAME/CLR NAME_sidechain.sdf
# Gaussian options
levelOfTheory B3LYP
basisSet 6-31G*
clusterCharge CLR 0
clusterSpin 1
gaussianNProc 2
gaussianMem 3000MB
# Set Gaussian input name --> Optimize and get force constants
gaussianOptAndFC /NAME/CLR NAME_sidechain.com
# Exit MCPB
quit
On Aug 27, 2014, at 1:33 AM, 高彧辉 <yuhuigao.mail.dlut.edu.cn> wrote:
> 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
>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> <sidechain.tar>_______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Wed Aug 27 2014 - 08:00:03 PDT
