Dear Francois,
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. So will the
unperturbed charge lead to any difficulty in creating the prmtop and inpcrd
files?
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.
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.
Thanx again for your help.
Sincerely
Nicholus
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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>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Thu May 03 2012 - 23:30:03 PDT
