Re: [AMBER] Metal parametrization problem!!

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Tue, 5 Aug 2014 16:33:05 -0400

Hi Pedro,

I don't think it is the Gaussian version you used to caused the problem
you mentioned in this email since the MCPB input file doesn't contain
any thing about the gaussian out file.

I agree with your guess. The main problem should be the amino acid residues
don't match in the between the large model and the standard model lib file or
the sidechain model parameter file.

When you created the standard model, did you include the PHE residue between
the two residues which bonded to iron?

BTW, where did you find the MKRadius of Iron? I also tried to find similar things online before
but could not find it.

All the best,
Pengfei

On Aug 5, 2014, at 1:56 PM, Pedro A. Baldera Aguayo <a.baldera7.gmail.com> wrote:

> Hi Pengfei,
>
> I've managed to find the MK Radii for Iron. At the beginning I tried to use
> a Gaussian keyword that generates this value in the G09 input file.
>
> Regarding the force constants, I'm not sure whether there is a problem with
> G09 A.01 because I generated the _sidechain_fc_sem.bcl.log from the fchk
> file that I got with that version of Gaussian.
>
> Now, I'm stuck on step 11, I'm not able to generate the
> _large_respgen.bcl.log. The error lies in that MCPB is unable to assign
> some parameters for bonds, angles and torsion, for example:
>
> ..
> Unable to assign parameters for bond : CZ - HZ
> Total Number of Missing Bond Parameters = 22
>
> ..
> Unable to assign parameters for angle: O - C - N
> Total Number of Missing Angle Parameters = 40
>
> ..
> Unable to assign parameters for torsion: CD1- CG - CD2- HD2
> Total Number of Missing Torsion Parameters = 65
>
> Is this error produced because MCPB is not reading the force constants
> parameters from the G09 A.01 log file?
>
> If not, I think that probably I made a mistake when generating the
> _large.bcl for Step 9 - Large Model Building because there are two residues
> (ASP49 and HIS51) that have exactly one residue between them (PHE50).
> Therefore, I added PHE50 as an extra residue in the following way:
>
> # Create ACE-1 from LYS-48
> createResidue ACE in CLR
> addToResidue /3PL1/CLR/ACE-1 /3PL1/1/LYS-48/.CA.
> setAtomName /3PL1/CLR/ACE-1/.CA. to .CH3
> addToResidue /3PL1/CLR/ACE-1 /3PL1/1/LYS-48/.C..
> addToResidue /3PL1/CLR/ACE-1 /3PL1/1/LYS-48/.O..
>
> # Create AS1-2 from ASP-49
> createResidue AS1 in CLR
> addToResidue /3PL1/CLR/AS1 /3PL1/1/ASP-49
>
> # Create PH1-3 from PHE-50
> createResidue PH1 in CLR
> addToResidue /3PL1/CLR/PH1 /3PL1/1/PHE-50
>
> # Create HDA-4 from HID-51
> createResidue HDA in CLR
> addToResidue /3PL1/CLR/HDA /3PL1/1/HID-51
>
> # Create NME-5 from ILE-52
> createResidue NME in CLR
> addToResidue /3PL1/CLR/NME-5 /3PL1/1/ILE-52/.N..
> addToResidue /3PL1/CLR/NME-5 /3PL1/1/ILE-52/.CA.
> setAtomName /3PL1/CLR/NME-5/.CA. to .CH3
>
> Please find attached the log files for respgen.bcl.log and _large.bcl.
>
> As always I would really appreciate your help
>
> Thank you!!
>
>
>
>
> 2014-08-04 21:46 GMT-05:00 Pedro A. Baldera Aguayo <a.baldera7.gmail.com>:
>
>> Hi Pengfei,
>>
>> Thanks for the advice. Right now I'm dealing with the large.bcl file. Most
>> of the examples provided by MCPB are for Zn; however for the
>>
>> setMKRadii zn 1.1
>>
>> I've been searching this value for Fe without success. Do I need to
>> provide this parameter by a Gaussian keyword?
>>
>> Best!
>>
>> Pedro
>>
>>
>> 2014-08-04 20:58 GMT-05:00 Pengfei Li <ambermailpengfei.gmail.com>:
>>
>> Hi Pedro,
>>>
>>> Sorry for one mistake in last email. I checked the version of G09 I used,
>>> it is G09-C1.
>>> MCPB does't support the force constant calculation using this version. I
>>> am not sure whether
>>> MCPB supports the G09-A1 version. You can try to test it.
>>>
>>> All the best,
>>> Pengfei
>>>
>>> On Aug 4, 2014, at 9:51 PM, Pengfei Li <ambermailpengfei.gmail.com>
>>> wrote:
>>>
>>>> Hi Pedro,
>>>>
>>>> For the force constant part calculation, it doesn't support Gaussian 09.
>>>> I recommended you to use Gaussian 03 to do the calculation. The support
>>>> for G09 are considered to be added in the future.
>>>>
>>>> For the RESP charge calculation, if you use the Gaussian09-C.01 or more
>>> recent
>>>> version you need to change the keyword IOp(6/33=2) to IOp(6/50=1) in
>>> the input file.
>>>> But for G09 Revision A.01 you don't need to change the keyword in the
>>> Gaussian
>>>> input file for RESP charge calculation.
>>>>
>>>> Hope it helps,
>>>> Pengfei
>>>>
>>>> On Aug 4, 2014, at 9:39 PM, "Pedro A. Baldera Aguayo" <
>>> a.baldera7.gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'd like to know if MCPB supports G09 Revision A.01?
>>>>>
>>>>> Thanks
>>>>>
>>>>> Pedro
>>>>>
>>>>>
>>>>> 2014-08-01 16:42 GMT-05:00 Pengfei Li <ambermailpengfei.gmail.com>:
>>>>>
>>>>>> Hi Pedro,
>>>>>>
>>>>>> MCPB may meet problems when adding the hydrogens for the water
>>> molecules.
>>>>>>
>>>>>> You can use tleap to add the hydrogens, it is pretty simple. Just type
>>>>>> following command in tleap:
>>>>>>>>>
>>>>>> source leaprc.ff99SB
>>>>>> mol = loadpdb Zn_L.pdb
>>>>>> savepdb mol Zn_L_addh.pdb
>>>>>> quit
>>>>>>>>>
>>>>>>
>>>>>> But the problem is the hydrogen adding to water molecules are not well
>>>>>> orientated. Which
>>>>>> may cause problem in the further gaussian calculation.
>>>>>>
>>>>>> You can use other software to add the hydrogen first.
>>>>>> Here is a webpage about that:
>>>>>>
>>> http://kpwu.wordpress.com/2012/02/24/add-protons-hydrogens-to-structure/
>>>>>> You can also use H++ website to add hydrogens:
>>>>>> http://biophysics.cs.vt.edu/
>>>>>> I tried to use WHAT IF and found it works well, both for protein
>>> hydrogens
>>>>>> and water hydrogens. You can try to begin from there.
>>>>>>
>>>>>> For the Zinc bonding site, I think you can try to use two waters to
>>>>>> generate the parameters.
>>>>>> MOH is for the hydroxyl group. Since there is only one metal site
>>> connect
>>>>>> to the 2 water oxygens,
>>>>>> it is fine to treat them as water but not OH groups.
>>>>>>
>>>>>> You can check the following directory:
>>>>>> $AMBERHOME/AmberTools/examples/mtkpp/MCPB/HHOO-1VLI/data/
>>>>>> Where there is a MCPB example of a metal site which congaing two HIS
>>> and
>>>>>> two water groups bonding to Zinc ion.
>>>>>>
>>>>>> Hope it helps, if you have other questions, please feel free to tell
>>> me.
>>>>>>
>>>>>> Best,
>>>>>> Pengfei
>>>>>>
>>>>>> On Aug 1, 2014, at 4:13 PM, Pedro A. Baldera Aguayo <
>>> a.baldera7.gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Jason,
>>>>>>>
>>>>>>> Thanks again for your answer. Yes, the water molecules are part of
>>> the
>>>>>>> metal complexes and what I did was following either MCPT or Pengfei's
>>>>>>> tutorial, and in the 2nd step, after typing:
>>>>>>>
>>>>>>> MCPB -i 3PL1_OH_addHs.bcl -l 3PL1_OH_addHs.bcl.log
>>>>>>>
>>>>>>> I got this message
>>>>>>>
>>>>>>> 1 Error in watProtonate ... exiting
>>>>>>> terminate called after throwing an instance of 'MTKpp::MTKException'
>>>>>>> Aborted (core dumped)
>>>>>>>
>>>>>>> And the message in the corresponding log file is:
>>>>>>>
>>>>>>> ### ### ### ###
>>>>>>> ### MTK++ Info ###
>>>>>>> ### Function: watProtonate::run ###
>>>>>>> ### Message: sorted water energies
>>>>>>> ### ### ### ###
>>>>>>>
>>>>>>> If you have any comments about this, please let me know. Of course,
>>> I'm
>>>>>>> still waiting for Pengfei because I think that he has already handled
>>>>>> this
>>>>>>> in a previous post.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Pedro
>>>>>>>
>>>>>>>
>>>>>>> 2014-08-01 14:27 GMT-05:00 Jason Swails <jason.swails.gmail.com>:
>>>>>>>
>>>>>>>> On Fri, Aug 1, 2014 at 2:38 PM, Pedro A. Baldera Aguayo <
>>>>>>>> a.baldera7.gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Yes, I did. However, I am facing problems with the wster molecules,
>>>>>> and I
>>>>>>>>> do not how to deal with them.
>>>>>>>>>
>>>>>>>>
>>>>>>>> ‚ÄčIf the water molecules are part of the metal complex, then I think
>>> that
>>>>>>>> MCPB should have added the necessary hydrogens in one of the steps
>>> (or
>>>>>> at
>>>>>>>> least there was a step to do so, if I recall correctly).
>>>>>>>>
>>>>>>>> If it's just a "typical" water molecule that is part of the bulk
>>> solvent
>>>>>>>> (or exchanges with the bulk solvent), then tleap should add those
>>>>>>>> automatically, assuming that the water residue is named correctly.
>>>>>>>>
>>>>>>>> Since I'm not super familiar with MCPB, I'll let Pengfei provide
>>> more
>>>>>>>> detailed answers if they're needed.
>>>>>>>>
>>>>>>>> Good luck,
>>>>>>>> Jason
>>>>>>>>
>>>>>>>> --
>>>>>>>> Jason M. Swails
>>>>>>>> BioMaPS,
>>>>>>>> Rutgers University
>>>>>>>> Postdoctoral Researcher
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Pedro A. Baldera-Aguayo
>>>>>>> National University of Engineering (UNI)
>>>>>>> Lima - Peru
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Pedro A. Baldera-Aguayo
>>>>> National University of Engineering (UNI)
>>>>> Lima - Peru
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> _______________________________________________
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>>>
>>
>>
>>
>> --
>> Pedro A. Baldera-Aguayo
>> National University of Engineering (UNI)
>> Lima - Peru
>>
>
>
>
> --
> Pedro A. Baldera-Aguayo
> National University of Engineering (UNI)
> Lima - Peru
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Received on Tue Aug 05 2014 - 14:00:02 PDT
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