Re: [AMBER] Metal parametrization problem!!

From: Pedro A. Baldera Aguayo <a.baldera7.gmail.com>
Date: Tue, 5 Aug 2014 12:56:10 -0500

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
>> >>>
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>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> 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 - 11:00:03 PDT
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