Dear community,
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.
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Thu Apr 19 2012 - 23:30:03 PDT
