Re: Re: [AMBER] error when doing MMPBSA

From: pxq <pangxueqintea.yahoo.com.cn>
Date: Tue, 23 Mar 2010 08:32:42 +0800

Ray,

    I have attached two of them behind, do they work?

Xueqin

======= 2010-03-23 00:54:40 您在来信中写道:=======

>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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>>
>> = = = = = = = = = = = = = = = = = = = =
>>
>>
>>         致
>> 礼!
>>
>>
>>         pxq
>>         pangxueqintea.yahoo.com.cn
>>           2010-03-22
>>
>>
>> ------------------------------------------------------------------------
>>
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        致
礼!
 
                                 
        pxq
        pangxueqintea.yahoo.com.cn
          2010-03-23


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Received on Mon Mar 22 2010 - 18:00:03 PDT
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