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 Wed May 02 2012 - 02:30:03 PDT
