AMBER Archive (2006)

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

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sat Jun 17 2006 - 15:37:46 CDT

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
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