AMBER Archive (2009)

Subject: [AMBER] Re: question_on_MMPBSA

From: jackie (youban.xm_at_gmail.com)
Date: Wed Aug 26 2009 - 10:08:01 CDT

>
>
>>
>>> Dear: ambers- MM-PBSA
>>>
>>>
>>> I have a quesiton on the MM-PBSA, when I start to do the
>>> decomposition for residues, the results confuse me a lot.
>>>
>>
>> for example, in a protein-protein complex,
>> if i choose 8 residues from the receptor and
>> 5 residues from the ligand(number 4-8). (all the 13 residues
>> located in the binding face)
>> at last, we will get a table of these 13 residues with delta G.
>>
>>>
>>> tBut, if we change the number of ligand to the
>>> whole ligand, 20 residues instead of 5. the result of delta G for
>>> these 5 residues in this time were totally different from results
>>> in the first run.
>>>
>>> also, i try the exmaple from 05_MMPBSA_Decomp_Residue
>>
>> the default is as below.
>> Residue
>>
>> 35 0.53 0.05 36 -0.04 0.26 37 9.84 0.8 38 7.08 0.63 39 2.14 0.17 40
>> 2.66 0.26 41 -3.14 0.76 175 -0.77 1 176 0.98 0.47 177 -2.06 0.52 178
>> -5.4 1.59 179 -7.48 0.47 180 -2.43 0.51
>> this the new one which contains all the residues, of course 35-41,
>> 175-180.
>> but i do not know why these values are not the same.
>>
>> Residue
>>> 1 0.66 2 0 3 -0.28 4 0.02 5 1.19 6 -0.04 7 0.01 8 -0.01 9 0.02
>>> 10 -0.03 11 -0.02 12 0.08 13 0.06 14 0.05 15 0.04 16 0.94 17 0.08
>>> 18 -0.03 19 0 20 0.08 21 -1.87 22 -0.02 23 0.05 24 -0.67 25 -2.23
>>> 26 0.06 27 0.22 28 0.01 29 -0.37 30 -0.38 31 -0.02 32 0.28 33
>>> 0.66 34 0.02 35 0.54 36 -2.41 37 -3.75 38 -1.07 39 -5.17 40 -4.82
>>> 41 -4.24 42 0.73 43 0.05 44 -0.01 45 0.01 46 0 47 -0.38 48 0 49
>>> -0.42 50 0.01 51 0.01 52 -0.07 53 -0.01 54 0.58 55 0 56 -0.26 57
>>> -0.35 58 0.2 59 0.09 60 0.02 61 0.09 62 -0.48 63 -0.42 64 0.19
>>> 65 0 66 0.02 67 -0.05 68 0.59 69 -0.52 70 0.24 71 0.01 72 -0.01
>>> 73 0.64 74 0.13 75 0.02 76 -0.49 77 0 78 0.01 79 -0.01 80 0.01
>>> 81 0.01 82 -0.01 83 0 84 0 85 0 86 0.01 87 0 88 0.48 89 0 90
>>> -0.01 91 -0.38 92 -0.49 93 -0.01 94 0.4 95 0 96 0.01 97 0.41 98
>>> -0.4 99 0 100 0 101 0.4 102 0.5 103 0.01 104 0.61 105 -0.43 106
>>> 0 107 -0.37 108 -0.39 109 0.01 110 -0.01 111 0.01 112 -0.01 113 0
>>> 114 0 115 0 116 0.03 117 0.64 118 0 119 -0.46 120 0.01 121 0 122
>>> 0 123 0.38 124 0 125 0 126 -0.33 127 0 128 0.29 129 0 130 0 131
>>> -0.01 132 -0.32 133 0 134 0 135 0.31 136 0 137 -0.01 138 0 139
>>> 0.01 140 -0.01 141 0 142 -0.01 143 -0.38 144 0.01 145 0.01 146
>>> 0.01 147 0.47 148 0 149 0.57 150 -0.01 151 0 152 0.01 153 -0.41
>>> 154 -0.41 155 0 156 -0.01 157 0.02 158 0.01 159 0 160 0 161 0.41
>>> 162 -0.4 163 0.01 164 0.42 165 0 166 0.04 167 0.77 168 -0.12 169
>>> -0.15 170 -4.66 171 -0.18 172 -0.14 173 -0.31 174 0.14 175 -1.89
>>> 176 -0.72 177 -2.94 178 -6.47 179 -6.09 180 -1.89 181 -0.38 182
>>> -0.05 183 0.1 184 -0.52 185 0.09 186 0.01 187 -0.04 188 0.02 189
>>> 0.05 190 -0.44 191 0.72 192 0.12 193 0.01 194 0.09 195 0.3 196
>>> -0.35 197 -0.18 198 -0.48 199 -2.82 200 -7.73 201 -0.61 202 0.1
>>> 203 0.06 204 -0.04 205 0.54 206 0.01 207 0.02 208 0.01 209 0.02
>>> 210 0 211 -0.43 212 0.01 213 0.01 214 0.08 215 0.37 216 -0.34 217
>>> -0.37 218 0 219 -0.33 220 -0.39 221 0 222 -0.37 223 0.01 224 0.41
>>> 225 0 226 0.01 227 0.01 228 0.5 229 0 230 0.02 231 0.01 232 0.03
>>> 233 0.03 234 0.05 235 0.6 236 1.07 237 0.02 238 0.08 239 0.02 240
>>> 0.53 241 0.04 242 0.38
>>>
>>>
>>>
>>> thanks
>>>
>>>
>>> jackie
>>>
>>> ELET UNIVERSITY HUNGARY
>>>
>>>
>>>
>>
>>
>>
>
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber