AMBER Archive (2003)

Subject: Re: AMBER: mgbjsb radii in GBSA

From: Junmei Wang (JWang_at_encysive.com)
Date: Tue Nov 11 2003 - 16:12:08 CST

In my opinion, prep input file doesn't provide any radii information and it
works for me when I load to leap. Maybe the function to assign radii dose
not recognize atom types outside of amber. For this simple molecule, why
not use amber atom types and do gbsa again, then you could find out if it
is the new atom types in gaff that causes this problem. To use amber atom
type, specify '-at amber' when you run antechamber.

Best

Junmei
===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             Giulio Rastelli
             <rastelli.giulio@
             unimo.it> To
             Sent by: amber_at_scripps.edu
             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       AMBER: mgbjsb radii in GBSA
             11/10/2003 10:39
             AM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

>Dear all,
>> I would like to calculate the binding energy of a protein-ligand
 complex
>> using GBSA. I created topologies of ligand, receptor and complex with
>> leap,
>> setting as default the mgbjsb radii (amber7) to be used with igb=4. The
>> ligand
>> uses the gaff force field, the protein uses ff99 and the complex uses
>> mixed
>> gaff+ff99.
>> While the GB energies of the receptor and of the complex seem ok, the
 GB
>> energy of the ligand is out of scale. I noticed that in the topology
>> file
>> of the ligand, the first atom has a radius of zero (which explains why
>> EGB
>> goes out of range) while the others are different from zero. Even if I
>> tried only for ten different molecules, it seems that when the first
>> atom
>> in the prep file belongs to a charged group (eg COO-, NH3+), its radius
>> is set to zero. Differently, all atoms have a non-zero radius, and GBSA
>> works
>> fine.
>> I include a prep file of a molecule that did NOT work, as an example.
>> Any ideas of why this could happen?
>> Thank you very much in advance for your help
>>
>> Giulio Rastelli
>>
>>
>> 0 0 2
>>
>> This is a remark line
>> molecule.res
>> <1> XYZ 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 O18 o M 3 2 1 1.540 111.208 180.000
 -0.604
>> 5 C12 c M 4 3 2 1.219 123.332 167.874
 0.131
>> 6 O19 o E 5 4 3 1.219 119.978 153.351
 -0.604
>> 7 C13 c3 M 5 4 3 1.507 119.986 -26.745
 0.004
>> 8 H32 hc E 7 5 4 1.090 109.508 29.965
 0.034
>> 9 H33 hc E 7 5 4 1.091 109.469 149.966
 0.034
>> 10 C14 c3 M 7 5 4 1.530 109.480 -90.059
 -0.033
>> 11 H34 hc E 10 7 5 1.089 109.509 -60.070
 0.028
>> 12 H35 hc E 10 7 5 1.090 109.467 59.966
 0.028
>> 13 C15 c3 M 10 7 5 1.531 109.466 179.949
 0.004
>> 14 H36 h1 E 13 10 7 1.090 109.499 60.050
 0.043
>> 15 H37 h1 E 13 10 7 1.089 109.469 -179.870
 0.043
>> 16 N16 n M 13 10 7 1.466 109.466 -59.902
 -0.114
>> 17 H38 hn E 16 13 10 0.971 119.981 -29.896
 0.131
>> 18 C17 c M 16 13 10 1.347 119.992 150.078
 0.248
>> 19 O20 o E 18 16 13 1.212 120.043 0.067
 -0.437
>> 20 C2 c3 M 18 16 13 1.507 119.968 -179.885
 0.141
>> 21 N1 n4 3 20 18 16 1.469 109.482 149.994
 0.145
>> 22 H21 hn E 21 20 18 1.009 109.471 179.932
 0.223
>> 23 H22 hn E 21 20 18 1.009 109.433 -60.043
 0.223
>> 24 H23 hn E 21 20 18 1.009 109.476 59.955
 0.223
>> 25 H24 hx E 20 18 16 1.090 109.534 29.977
 0.070
>> 26 C3 c3 M 20 18 16 1.530 109.436 -90.015
 0.009
>> 27 H25 hc E 26 20 18 1.090 109.459 -60.032
 0.034
>> 28 H26 hc E 26 20 18 1.090 109.482 60.011
 0.034
>> 29 C4 ca M 26 20 18 1.507 109.467 -179.954
 -0.054
>> 30 C5 ca M 29 26 20 1.383 119.883 -90.017
 -0.041
>> 31 H27 ha E 30 29 26 1.080 120.029 -0.034
 0.065
>> 32 C6 ca M 30 29 26 1.386 119.989 179.984
 0.086
>> 33 O11 oh S 32 30 29 1.360 120.061 179.969
 -0.316
>> 34 H31 ho E 33 32 30 0.967 106.795 90.029
 0.218
>> 35 C7 ca M 32 30 29 1.391 119.839 0.010
 0.086
>> 36 O8 oh S 35 32 30 1.360 120.085 179.986
 -0.316
>> 37 H28 ho E 36 35 32 0.967 106.796 89.939
 0.218
>> 38 C9 ca M 35 32 30 1.386 119.867 0.003
 -0.044
>> 39 H29 ha E 38 35 32 1.080 119.966 -179.986
 0.065
>> 40 C10 ca M 38 35 32 1.382 119.992 -0.312
 -0.068
>> 41 H30 ha E 40 38 35 1.080 119.952 -179.681
 0.063
>>
>>
>> LOOP
>> C10 C4
>>
>> IMPROPER
>> C13 O18 C12 O19
>> C2 N16 C17 O20
>> C3 C5 C4 C10
>> C4 C6 C5 H27
>> C5 C7 C6 O11
>> C6 C9 C7 O8
>> C7 C10 C9 H29
>> C4 C9 C10 H30
>>
>> DONE
>> STOP 

--

Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Universita di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
-------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
-------------------------------------

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