Re: Re: Re: [AMBER] error when doing MMPBSA

From: pxq <pangxueqintea.yahoo.com.cn>
Date: Wed, 24 Mar 2010 08:43:18 +0800

Ray,

   Thank you for your suggestions

Best wishes

        

======= 2010-03-23 12:43:10 您在来信中写道:=======

>The output files clearly show that you didn't clean up the folder after
>previous failures. I can see multiple energy printout for snapshot #1 and so
>on. Please clean up before you try again.
>
>Also, a often repeated suggestion on the mailing list is that please go
>through one example mmpbsa job BY HAND to make sure you understand the data
>flow that is automated by the script.
>
>All the best,
>Ray
>
>2010/3/22 pxq <pangxueqintea.yahoo.com.cn>
>
>> 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
>> >>>>
>> ===========================================================================
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> __________________________________________________
>> >>>> 赶快注册雅虎超大容量免费邮箱?
>> >>>> http://cn.mail.yahoo.com
>> >>>>
>> >>>>
>> >>>> _______________________________________________
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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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= = = = = = = = = = = = = = = = = = = =
                        

        致
礼!
 
                                 
        pxq
        pangxueqintea.yahoo.com.cn
          2010-03-24

嗃i'櫒ド╤∈&

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Received on Tue Mar 23 2010 - 18:00:03 PDT
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