AMBER Archive (2003)

Subject: AMBER: mgbjsb Radii in GBSA

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Tue Oct 07 2003 - 09:42:34 CDT

> 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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