AMBER Archive (2006)

Subject: Fwd: Fwd: Fwd: AMBER: LEaP error : unbalanced charge

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sun Jun 18 2006 - 08:17:57 CDT

Dear IIyas

I am not clear about "Constrain the charges of the JOINT atoms to the given
AMBER charges of the JOINT atoms". You said that "I specified for this new
residue in the QM calculation". So, please give me more specific details to
do that. Because I am just the beginner to use amber. It would be very nice
if you can help me again.

Thanks in advance for any helps,

Best regards,

Jitrayut

---------- Forwarded message ----------
From: Ilyas Yildirim <yildirim_at_pas.rochester.edu>
Date: 18 ÁÔ.Â. 2006, 14:53 ¹.
Subject: Re: Fwd: Fwd: AMBER: LEaP error : unbalanced charge
To: amber_at_scripps.edu
Cc: steinbrt_at_scripps.edu

Dear jitrayut,

The easiest way to get the resp charges would be the following: Create
your new residue, which will have only the joint atoms. Then do the
quantum mechanical calculations to get the ESP Data points (be sure to
specify the total charge of the residue while using Gaussian). After
that, u need to use 'resp' to get the charges. Constrain the charges of
the JOINT atoms to the given AMBER charges of the JOINT atoms. This will
create the charges such that when your new residue is part of a structure,
the joint points will have the same charge. And the effect of the new
residue on the TOTAL charge of the structure is going to be the total
charge u specified for this new residue in the QM calculation. This is the
easiest way to get the resp charges for a mutated structure. Good luck.

Best,

PS: It is always good to use the same atom name nomenclature when
creating a new (mutated) residue.

On Sun, 18 Jun 2006, jitrayut jitonnom wrote:

> Dear Thomas
>
> This is the resp charge (A)comparing with the regular tyrosine residue
> (B) see below. It can be seen that some atoms were not make sense. So,
this
> should be error for resp calculation ? ,if yes, how to fixed this ? By the
> way,I though the reason why I got the total charges about -17.48xx because
I
> cut the H9 and H10 atom to make peptide bond before do leap. However, I am
> still not sure that this would be the right method for making deprotonate
> tyrosine by using resp charge. So, any suggestions would be great and i
will
> be very appreciated.
>
> Note : the atom types here are different so please check carefully.
>
> A. prepin file
> 0 0 2
> This is a remark line
> molecule.res
> TYD INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 O2 O M 3 2 1 1.540 111.208 180.000 -0.53439
> 5 C9 C M 4 3 2 1.191 63.576 -120.918 0.41332
> 6 H10 HA E 5 4 3 1.097 120.298 179.059 -0.00845
> 7 C1 CT M 5 4 3 1.514 126.028 -0.066 0.53319
> 8 N1 NT B 7 5 4 1.459 107.287 -143.816 -1.13600
> 9 H1 H E 8 7 5 1.005 109.207 78.300 0.39589
> 10 H9 H E 8 7 5 1.002 108.143 -167.941 0.39589
> 11 H2 H1 E 7 5 4 1.090 104.755 103.735 -0.01742
> 12 C2 CT M 7 5 4 1.539 113.923 -14.494 -0.25965
> 13 H3 HC E 12 7 5 1.089 107.981 -60.111 0.05133
> 14 H4 HC E 12 7 5 1.087 107.917 53.882 0.05133
> 15 C3 CA M 12 7 5 1.512 113.246 177.525 -0.05391
> 16 C4 CA M 15 12 7 1.401 121.862 -79.891 -0.11189
> 17 H5 HA E 16 15 12 1.083 118.690 -2.742 0.09474
> 18 C5 CA M 16 15 12 1.372 122.821 177.593 -0.50301
> 19 H6 HA E 18 16 15 1.078 120.274 179.653 0.14397
> 20 C6 C M 18 16 15 1.440 122.622 0.035 0.72384
> 21 O1 O E 20 18 16 1.243 123.226 -179.777 -0.80261
> 22 C7 CA M 20 18 16 1.438 113.346 0.438 -0.50301
> 23 H7 HA E 22 20 18 1.079 117.149 179.035 0.14397
> 24 C8 CA M 22 20 18 1.375 122.532 -0.424 -0.11189
> 25 H8 HA E 24 22 20 1.084 118.354 179.428 0.09474
> LOOP
> C8 C3
> IMPROPER
> C1 H10 C9 O2
> C4 C8 C3 C2
> C3 C5 C4 H5
> C6 C4 C5 H6
> C5 C7 C6 O1
> C6 C8 C7 H7
> C3 C7 C8 H8
> DONE
> STOP
> B. regular tyrosine residue
>
>
> !entry.TYR.unit.atoms table str name str type int typex int resx int flags
> int seq int elmnt dbl chg
>
> "N" "N" 0 1 131072 1 7 -0.415700
>
> "H" "H" 0 1 131072 2 1 0.271900
>
> "CA" "CT" 0 1 131072 3 6 -0.001400
>
> "HA" "H1" 0 1 131072 4 1 0.087600
>
> "CB" "CT" 0 1 131072 5 6 -0.015200
>
> "HB2" "HC" 0 1 131072 6 1 0.029500
>
> "HB3" "HC" 0 1 131072 7 1 0.029500
>
> "CG" "CA" 0 1 131072 8 6 -0.001100
>
> "CD1" "CA" 0 1 131072 9 6 -0.190600
>
> "HD1" "HA" 0 1 131072 10 1 0.169900
>
> "CE1" "CA" 0 1 131072 11 6 -0.234100
>
> "HE1" "HA" 0 1 131072 12 1 0.165600
>
> "CZ" "C" 0 1 131072 13 6 0.322600
>
> "OH" "OH" 0 1 131072 14 8 -0.557900
>
> "HH" "HO" 0 1 131072 15 1 0.399200
>
> "CE2" "CA" 0 1 131072 16 6 -0.234100
>
> "HE2" "HA" 0 1 131072 17 1 0.165600
>
> "CD2" "CA" 0 1 131072 18 6 -0.190600
>
> "HD2" "HA" 0 1 131072 19 1 0.169900
>
> "C" "C" 0 1 131072 20 6 0.597300
>
> "O" "O" 0 1 131072 21 8 -0.567900
>
>
> Jitrayut Jitonnom, Ph.D.(candidate)
> Dept. of Chemistry,
> Computational Simulation,
> and Modeling Laboratory (CSML),
> Chiang Mai University, Thailand.
> Tel: +66(0)6613-4218
> Email: jitrayut.018_at_gmail.com <shafinaz_at_bri.nrc.ca>
>
http://www.science.cmu.ac.th/department/chemistry/Research%20groups/CSML/index.htm
>
>
> ---------- Forwarded message ----------
> From: jitrayut jitonnom <jitrayut.018_at_gmail.com>
> Date: 17 ÁÔ.Â. 2006, 0:28 ¹.
> Subject: Fwd: Fwd: AMBER: LEaP error : unbalanced charge
> To: amber_at_scripps.edu, steinbrt_at_scripps.edu
>
> Dear Thomas
>
> I am not sure that I had done right for deprotonate tyrosine. But I can
only
> give you some details that I try to check this charge. I see the partial
> charge from WeblabViewer and it has decrease comparing with regular
> tyrosine. For the prepin file, I see this charges do not have the same
> charge. I think this charge from prepin file should be ok. Besides, I had
> already edited atom C and O (C=O)that link the peptide bond with N-H to
link
> the peptide bond. I mean I found the peptide bond breaking down when I do
> LEaP without C-O modified. So I decide to change C2-O5 to C-O to every
> parameter files generated by antechamber. This can link this peptide bond.
> Hopefully all of these details maybe give you an idea that why I do wrong
> with this charges. Maybe, this is not the way to do RESP charge.
Therefore,
> please tell me the the right one.
>
> Thanks
>
> Jitrayut
>
> ---------- Forwarded message ----------
> From: Thomas Steinbrecher <steinbrt_at_scripps.edu >
> Date: 16 ÁÔ.Â. 2006, 23:45 ¹.
> Subject: Re: Fwd: AMBER: LEaP error : unbalanced charge
> To: jitrayut jitonnom <jitrayut.018_at_gmail.com>
>
> Hi,
>
> you should have created a .lib or .prep file for your new residue. Load
> this into leap and edit it. You can set leap to display the charges for
> you.
>
> Regards,
>
> Thomas
> 

--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty       -                              -
- University of Rochester      -                              -
- Hutchison Hall, # B10        -                              -
- Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/                     -
---------------------------------------------------------------

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