Re: [AMBER] Metal parametrization problem!!

From: Pedro A. Baldera Aguayo <a.baldera7.gmail.com>
Date: Tue, 5 Aug 2014 16:01:25 -0500

Hi Pengfei,

Thanks for your reply.

No, I did not add the PHE residue in the standard model libe file neither
the sidechain model. I've also realized that before I got your email. I'll
let you know if everything works.

I found the MKRadius of Iron (+2/+3) in the attached paper.

Best,

Pedro



2014-08-05 15:45 GMT-05:00 Pedro A. Baldera Aguayo <a.baldera7.gmail.com>:

> Hi Pengfei,
>
> Thanks for your reply.
>
> No, I did not add the PHE residue in the standard model libe file neither
> the sidechain model. I've also realized that before I got your email. I'll
> let you know if everything works.
>
> I found the MKRadius of Iron (+2/+3) in the attached paper.
>
> Best,
>
> Pedro
>
>
> 2014-08-05 15:33 GMT-05:00 Pengfei Li <ambermailpengfei.gmail.com>:
>
> 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
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>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>>> Pedro A. Baldera-Aguayo
>> >>>>> National University of Engineering (UNI)
>> >>>>> Lima - Peru
>> >>>>> _______________________________________________
>> >>>>> AMBER mailing list
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>> >>>>
>> >>>
>> >>>
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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
>> >
>> <3PL1_large_respgen.bcl.log><3PL1_large.bcl>_______________________________________________
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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 - 14:30:02 PDT
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