Dear Nicholus,
> Thank you for the reply. Actually I am performing constant pH simulation of
> a protein which contains a Ca atom. I have used ff99SB force field for
> this. I have performed Constant pH simulation of the protein without Ca
> atom and there was no problem. Since CpHMD is performed in implicit solvent
> neither any water molecule nor any counterions are added.
In implicit solvent conditions, you are NOT in periodic conditions
(solvent box) i. e. your system is not solvated by explicit solvent
molecules and no counterions are required to be added to neutralize
your molecular system.
That being said and I might be wrong but my understanding is that you
can run MD simulations with water molecules and/or with a Calcium atom
localized at well defined positions in implicit and explicit solvent
conditions...
I am sure people in this list will better explain that than me.
> So will the
> unperturbed charge lead to any difficulty in creating the prmtop and inpcrd
> files?
No
> As mentioned in the previous mail I have performed the procedure as
> mentioned in the tutorial "Simulating a Solvated Protein that Contains
> Non-Standard Residues" by Ross Walker. Since in that tutorial Cu atom was
> connected to Nitrogen and Sulphur atoms. In my case Ca atom is connected to
> Oxygen atoms. So while creating the prmtop and inpcrd files it is asking
> for Ca-OH parameters rather than Ca-O parameters. How should I deal with
> this problem.
I did not read this tutorial written by Ross.
My understanding is that an hydroxyl group does not interact with a
metal but an alcoholate does. If you indeed have an alcoholate
connected to a metal atom (Calcium) for sure the atom type of the
oxygen atom is not 'OH'.
For the definition of the atom types for the oxygen atoms connected to
a Fe3+ center, see
http://q4md-forcefieldtools.org/REDDB/projects/F-88/
&
http://q4md-forcefieldtools.org/REDDB/projects/F-88/script1.ff
More generally, see Cornell et al. J.Am.Chem.Soc. 1995,117,5179-51977
Table 1. List of Atom Types page 5182.
OH sp3 oxygen in alcohols, tyrosine
O2 sp2 oxygen in anionic acids
Nicholus: you need to understand what these atom types mean. Then, you
can use/read a tutorial...
> One last thing. I have used the simple protocol where only the metal atom
> is isolated to create new frcmod file. In the advance tutorial the metal
> atom together with the residues which are connected with it are isolated to
> create frcmod file. Should I revert to this advance protocol.
Once again you could read:
http://q4md-forcefieldtools.org/REDDB/projects/F-88/
Personally, I vote for computing the entire complex by QM: the total
charge of the metal being constrained (or not) to its integer value
(+2 for Ca2+)...
That being said the cpu time required in this case can be very
important. This is a reason why we have created R.E.D. Server .
http://q4md-forcefieldtools.org/REDS/
I hope this helps.
regards, Francois
> On Wed, May 2, 2012 at 2:55 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Nicholus,
>>
>> After a quick look, we can see different problems:
>> - WARNING: The unperturbed charge of the unit: -3.003600 is not zero.
>> -> this is likely a rounding off error of .0036
>> I would check that as this might reflect a more important problem.
>> (in general a rounding off error is of +/-5.10-4; depending on the
>> accuracy required: 10-3 or 10-4...)
>>
>> - Many FF parameters are missing...
>> did you load a FF parameter (before) your frcmod file?
>>
>> - It looks like you have errors in the FF atom type definition:
>> Could not find angle parameter: C - OH - CA
>> -> I might be wrong but it is unlikely that an hydroxyl group is
>> connected to a calcium atom; is it not an alcoholate ? if so the atom
>> type you used is wrong: 'OH' is for an oxygen atom in an alcohol
>> function...
>>
>> Could not find angle parameter: HO - OH - HO
>> -> do you have a water molecule that is not a TIP3P molecule?
>>
>> To better help we would need the FF name you wish use...
>>
>> regards, Francois
>>
>>
>>
>> > I am trying to create prmtop and inpcrd files for simulation of a
>> > protein containing one calcium atom. For this I have used the
>> > procedure given in the tutorial "Simulating a Solvated Protein that
>> > Contains Non-Standard Residues" by Ross Walker. I am just facing
>> > problem in the last step i.e. including the parameter for calcium.
>> >
>> > ******************************
>> > **************************************************************
>> > Before including the parameter for calcium (through try.frcmod) my
>> > tleap out shows the following
>> >
>> >
>> >> loadoff mol.lib
>> >> check mol
>> > Checking 'mol'....
>> > WARNING: The unperturbed charge of the unit: -3.003600 is not zero.
>> > WARNING: The perturbed charge: -3.003600 is not zero.
>> > Warning: Close contact of 1.098314 angstroms between .R<AS4 16>.A<HD12
>> > 19> and .R<LEU 23>.A<H 2>
>> > Warning: Close contact of 2.208809 angstroms between .R<TYR 18>.A<HH
>> > 15> and .R<AS4 97>.A<HD11 18>
>> > Warning: Close contact of 1.630111 angstroms between .R<ASN 71>.A<HD21
>> > 11> and .R<ILE 75>.A<H 2>
>> > Warning: Close contact of 1.930749 angstroms between .R<AS4 88>.A<HD12
>> > 19> and .R<AS4 88>.A<H 2>
>> > Warning: Close contact of 2.051907 angstroms between .R<AS4
>> > 102>.A<HD12 19> and .R<AS4 102>.A<H 2>
>> > Warning: Close contact of 2.083472 angstroms between .R<GL4 121>.A<HB3
>> > 7> and .R<LYS 122>.A<H 2>
>> > Checking parameters for unit 'mol'.
>> > Checking for bond parameters.
>> > Could not find bond parameter for: O - CA
>> > No bond parameter for: O - CA
>> > Could not find bond parameter for: O - CA
>> > No bond parameter for: O - CA
>> > Checking for angle parameters.
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: O - CA - OH
>> > Can't find angle parameter: O - CA - OH
>> > Could not find angle parameter: O - CA - O
>> > Can't find angle parameter: O - CA - O
>> > Could not find angle parameter: O - CA - OH
>> > Can't find angle parameter: O - CA - OH
>> > Could not find angle parameter: O - CA - OH
>> > Can't find angle parameter: O - CA - OH
>> > Could not find angle parameter: C - O - CA
>> > Can't find angle parameter: C - O - CA
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: C - OH - CA
>> > Can't find angle parameter: C - OH - CA
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - CA - O
>> > Can't find angle parameter: OH - CA - O
>> > Could not find angle parameter: OH - CA - OH
>> > Can't find angle parameter: OH - CA - OH
>> > Could not find angle parameter: OH - CA - OH
>> > Can't find angle parameter: OH - CA - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: C - O - CA
>> > Can't find angle parameter: C - O - CA
>> > Could not find angle parameter: O - CA - OH
>> > Can't find angle parameter: O - CA - OH
>> > Could not find angle parameter: O - CA - OH
>> > Can't find angle parameter: O - CA - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: C - OH - CA
>> > Can't find angle parameter: C - OH - CA
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - CA - OH
>> > Can't find angle parameter: OH - CA - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: C - OH - CA
>> > Can't find angle parameter: C - OH - CA
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: HO - OH - HO
>> > Could not find angle parameter: OH - C - OH
>> > There are missing parameters.
>> > check: Warnings: 8
>> > Unit is OK.
>> >
>> **********************************************************************************************
>> >
>> >
>> > My try.frcmod file is as below:
>> >
>> > # modifications to force field for alpha-lactalbumin
>> >
>> > MASS
>> > CA 40.08
>> >
>> > BOND
>> > O-CA 402.100 2.6
>> >
>> > ANGLE
>> > O-CA-OH 50.000 126.700
>> > O-CA-O 50.000 126.700
>> > C-O-CA 50.000 120.000
>> > C-OH-CA 50.000 120.000
>> > HO-OH-HO 50.000 120.000
>> > HO-C-HO 50.000 120.000
>> >
>> > DIHE
>> > X-O-CA-X 1 0.000 180.000 3.000
>> > X-OH-CA-X 1 0.000 180.000 3.000
>> >
>> > NONBON
>> > CA 1.79 0.200
>> >
>> >
>> ********************************************************************************************
>> >
>> > After including the try.frcmod file my tleap output is as follows:
>> >
>> >
>> >> loadamberparams try.frcmod
>> >> loadoff mol.lib
>> >> check mol
>> > Checking 'mol'....
>> > WARNING: The unperturbed charge of the unit: -3.003600 is not zero.
>> > WARNING: The perturbed charge: -3.003600 is not zero.
>> > Warning: Close contact of 1.098314 angstroms between .R<AS4 16>.A<HD12
>> > 19> and .R<LEU 23>.A<H 2>
>> > Warning: Close contact of 2.208809 angstroms between .R<TYR 18>.A<HH
>> > 15> and .R<AS4 97>.A<HD11 18>
>> > Warning: Close contact of 1.630111 angstroms between .R<ASN 71>.A<HD21
>> > 11> and .R<ILE 75>.A<H 2>
>> > Warning: Close contact of 1.930749 angstroms between .R<AS4 88>.A<HD12
>> > 19> and .R<AS4 88>.A<H 2>
>> > Warning: Close contact of 2.051907 angstroms between .R<AS4
>> > 102>.A<HD12 19> and .R<AS4 102>.A<H 2>
>> > Warning: Close contact of 2.083472 angstroms between .R<GL4 121>.A<HB3
>> > 7> and .R<LYS 122>.A<H 2>
>> > Checking parameters for unit 'mol'.
>> > Checking for bond parameters.
>> > Checking for angle parameters.
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - CA - OH
>> > Can't find angle parameter: OH - CA - OH
>> > Could not find angle parameter: OH - CA - OH
>> > Can't find angle parameter: OH - CA - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - CA - OH
>> > Can't find angle parameter: OH - CA - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > Could not find angle parameter: OH - C - OH
>> > There are missing parameters.
>> > check: Warnings: 8
>> > Unit is OK.
>> >
>> ******************************************************************************************
>> >
>> > Kindly let me know in which part I am making mistake. Thank you in
>> advance.
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Received on Fri May 04 2012 - 06:30:02 PDT
