Not the log files, I want to see your .out files such as "pro-A_rec.all.out" and "pro-B_com.all.out". These are the raw data before going to mmpbsa statistical analysis.
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor in Computational
Biochemistry and Molecular Biophysics
Dept of Molecular Biology and Biochemistry
Dept of Biomedical Engineering
University of California, Irvine, CA 92697-3900
Email: rluo.uci.edu Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/rayl/
==========================================
pxq wrote:
> Ray Luo,您好！
>
> The error report this time is:
> No data for 0+2 MM BOND 400
> No data for 0+2 MM BOND 300
> No data for 0+2 MM BOND 300
>
> And exit with "Exit 26"
>
> Becauese of the field size limitation of Amberlist, I only attach one of the outputs behind. If needed I can attach others in another e-mail )
>
> The difference between the first and second outputs of the same system is:
>
>
>> 1185a1186,1188
>> WARNING: Missing PBCAV for PB in 390 -> Taken from 389
>> WARNING: Missing PBDIS for PB in 390 -> Taken from 389
>> WARNING: Missing SURF for MS in 390 -> Taken from 389
>>
>
> And differ the outputs of different system get the follows:
>
> WARNING: Missing PBCAV for PB in 40 -> Taken from 39
> < WARNING: Missing PBDIS for PB in 40 -> Taken from 39
> < WARNING: Missing SURF for MS in 40 -> Taken from 39
> < WARNING: Missing PBCAV for PB in 62 -> Taken from 61
> < WARNING: Missing PBDIS for PB in 62 -> Taken from 61
> < WARNING: Missing SURF for MS in 62 -> Taken from 61
> < WARNING: Missing PBCAV for PB in 140 -> Taken from 139
> < WARNING: Missing PBDIS for PB in 140 -> Taken from 139
> < WARNING: Missing SURF for MS in 140 -> Taken from 139
> < WARNING: Missing PBCAV for PB in 162 -> Taken from 161
> < WARNING: Missing PBDIS for PB in 162 -> Taken from 161
> < WARNING: Missing SURF for MS in 162 -> Taken from 161
> < WARNING: Missing PBCAV for PB in 240 -> Taken from 239
> < WARNING: Missing PBDIS for PB in 240 -> Taken from 239
> < WARNING: Missing SURF for MS in 240 -> Taken from 239
> < WARNING: Missing PBCAV for PB in 262 -> Taken from 261
> < WARNING: Missing PBDIS for PB in 262 -> Taken from 261
> < WARNING: Missing SURF for MS in 262 -> Taken from 261
> < WARNING: Missing PBCAV for PB in 340 -> Taken from 339
> < WARNING: Missing PBDIS for PB in 340 -> Taken from 339
> < WARNING: Missing SURF for MS in 340 -> Taken from 339
> < WARNING: Missing PBCAV for PB in 390 -> Taken from 389
> < WARNING: Missing PBDIS for PB in 390 -> Taken from 389
> < WARNING: Missing SURF for MS in 390 -> Taken from 389
> < Reading pro-A_rec.all.out
> ---
>
>> Reading pro-B_com.all.out
>> WARNING: Missing PBCAV for PB in 80 -> Taken from 79
>> WARNING: Missing PBDIS for PB in 80 -> Taken from 79
>> WARNING: Missing SURF for MS in 80 -> Taken from 79
>> WARNING: Missing PBCAV for PB in 180 -> Taken from 179
>> WARNING: Missing PBDIS for PB in 180 -> Taken from 179
>> WARNING: Missing SURF for MS in 180 -> Taken from 179
>> WARNING: Missing PBCAV for PB in 280 -> Taken from 279
>> WARNING: Missing PBDIS for PB in 280 -> Taken from 279
>> WARNING: Missing SURF for MS in 280 -> Taken from 279
>> WARNING: Missing PB for PB in 300 -> Taken from 299
>> WARNING: Missing PBCAV for PB in 300 -> Taken from 299
>> WARNING: Missing PBDIS for PB in 300 -> Taken from 299
>> WARNING: Missing SURF for MS in 300 -> Taken from 299
>> WARNING: Missing PB for PB in 301 -> Taken from 300
>> WARNING: Missing PBCAV for PB in 301 -> Taken from 300
>> WARNING: Missing PBDIS for PB in 301 -> Taken from 300
>> WARNING: Missing SURF for MS in 301 -> Taken from 300
>> WARNING: Missing PBCAV for PB in 382 -> Taken from 381
>> WARNING: Missing PBDIS for PB in 382 -> Taken from 381
>> WARNING: Missing SURF for MS in 382 -> Taken from 381
>> Reading pro_B_rec.all.out
>>
> 1192,1202c1188,1231
> < WARNING: Missing PB for PB in 37 -> Taken from 36
> < WARNING: Missing PBCAV for PB in 37 -> Taken from 36
> < WARNING: Missing PBDIS for PB in 37 -> Taken from 36
> < WARNING: Missing SURF for MS in 37 -> Taken from 36
> < WARNING: Missing PBCAV for PB in 100 -> Taken from 99
> < WARNING: Missing PBDIS for PB in 100 -> Taken from 99
> < WARNING: Missing SURF for MS in 100 -> Taken from 99
> < WARNING: Missing PBCAV for PB in 200 -> Taken from 199
> < WARNING: Missing PBDIS for PB in 200 -> Taken from 199
> < WARNING: Missing SURF for MS in 200 -> Taken from 199
> < Reading pro-A_lig.all.out
> ---
>
>> WARNING: Missing PB for PB in 8 -> Taken from 7
>> WARNING: Missing PBCAV for PB in 8 -> Taken from 7
>> WARNING: Missing PBDIS for PB in 8 -> Taken from 7
>> WARNING: Missing SURF for MS in 8 -> Taken from 7
>> WARNING: Missing PBCAV for PB in 26 -> Taken from 25
>> WARNING: Missing PBDIS for PB in 26 -> Taken from 25
>> WARNING: Missing SURF for MS in 26 -> Taken from 25
>> WARNING: Missing PBCAV for PB in 29 -> Taken from 28
>> WARNING: Missing PBDIS for PB in 29 -> Taken from 28
>> WARNING: Missing SURF for MS in 29 -> Taken from 28
>> WARNING: Missing PBCAV for PB in 89 -> Taken from 88
>> WARNING: Missing PBDIS for PB in 89 -> Taken from 88
>> WARNING: Missing SURF for MS in 89 -> Taken from 88
>> WARNING: Missing PBCAV for PB in 126 -> Taken from 125
>> WARNING: Missing PBDIS for PB in 126 -> Taken from 125
>> WARNING: Missing SURF for MS in 126 -> Taken from 125
>> WARNING: Missing PBCAV for PB in 129 -> Taken from 128
>> WARNING: Missing PBDIS for PB in 129 -> Taken from 128
>> WARNING: Missing SURF for MS in 129 -> Taken from 128
>> WARNING: Missing PBCAV for PB in 189 -> Taken from 188
>> WARNING: Missing PBDIS for PB in 189 -> Taken from 188
>> WARNING: Missing SURF for MS in 189 -> Taken from 188
>> WARNING: Missing PBCAV for PB in 226 -> Taken from 225
>> WARNING: Missing PBDIS for PB in 226 -> Taken from 225
>> WARNING: Missing SURF for MS in 226 -> Taken from 225
>> WARNING: Missing PBCAV for PB in 229 -> Taken from 228
>> WARNING: Missing PBDIS for PB in 229 -> Taken from 228
>> WARNING: Missing SURF for MS in 229 -> Taken from 228
>> WARNING: Missing PBCAV for PB in 289 -> Taken from 288
>> WARNING: Missing PBDIS for PB in 289 -> Taken from 288
>> WARNING: Missing SURF for MS in 289 -> Taken from 288
>> WARNING: Missing PBCAV for PB in 326 -> Taken from 325
>> WARNING: Missing PBDIS for PB in 326 -> Taken from 325
>> WARNING: Missing SURF for MS in 326 -> Taken from 325
>> WARNING: Missing PBCAV for PB in 329 -> Taken from 328
>> WARNING: Missing PBDIS for PB in 329 -> Taken from 328
>> WARNING: Missing SURF for MS in 329 -> Taken from 328
>> WARNING: Missing PBCAV for PB in 376 -> Taken from 375
>> WARNING: Missing PBDIS for PB in 376 -> Taken from 375
>> WARNING: Missing SURF for MS in 376 -> Taken from 375
>> WARNING: Missing PBCAV for PB in 379 -> Taken from 378
>> WARNING: Missing PBDIS for PB in 379 -> Taken from 378
>> WARNING: Missing SURF for MS in 379 -> Taken from 378
>>
>
> ======= 2010-03-22 03:06:29 您在来信中写道：=======
>
>
>> Xueqin,
>>
>> Can you share your ".out" files for the run for both cases?
>>
>> All the best,
>> Ray
>>
>> ==========================================
>> Ray Luo, Ph.D.
>> Associate Professor in Computational
>> Biochemistry and Molecular Biophysics
>> Dept of Molecular Biology and Biochemistry
>> Dept of Biomedical Engineering
>> University of California, Irvine, CA 92697-3900
>> Email: rluo.uci.edu Phones: (949) 824-9528, 9562
>> Web: http://rayl0.bio.uci.edu/rayl/
>> ==========================================
>>
>>
>>
>> pxq wrote:
>>
>>> Hello everyone,
>>>
>>> When doing MMPBSA for pb-sa calculation I all way get the error reports:"No data for 0+2 MM BOND 200"
>>>
>>> And this time I tried the patched MMPBSA from Mengjuei Hsieh and further split my dcd into two parts, snapshots for 1-50 and 51-100. It is ok when calculate the 51-100 snapshots, but get the following error report when calculate the 1-50 ones.
>>>
>>> The errors are:
>>> No data for 0+2 MM BOND 300
>>> No data for 0+2 MM BOND 250
>>>
>>> So, do you have any suggestions on this problem? Thanks so much for your kind help
>>>
>>> Xueqin
>>>
>>> ===========================================================================
>>> Pang Xueqin
>>> State Key Laboratory of Molecular Reaction Dynamics
>>> Dalian Institute of Chemical Physics
>>> Chinese Academy of Sciences.
>>> Tel: 0411-84379352 Fax: 0411-84675584
>>> ===========================================================================
>>>
>>>
>>>
>>>
>>> __________________________________________________
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>>>
>>>
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>>>
>>>
>>>
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>>
>
> = = = = = = = = = = = = = = = = = = = =
>
>
> 致
> 礼！
>
>
> pxq
> pangxueqintea.yahoo.com.cn
> 2010-03-22
>
>
> ------------------------------------------------------------------------
>
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Received on Mon Mar 22 2010 - 10:00:03 PDT
