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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> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >> = = = = = = = = = = = = = = = = = = = =
> >>
> >>
> >> 致
> >> 礼！
> >>
> >>
> >> pxq
> >> pangxueqintea.yahoo.com.cn
> >> 2010-03-22
> >>
> >>
> >> ------------------------------------------------------------------------
> >>
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> >>
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>
> = = = = = = = = = = = = = = = = = = = =
>
>
> 致
> 礼！
>
>
> pxq
> pangxueqintea.yahoo.com.cn
> 2010-03-23
>
>
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Received on Mon Mar 22 2010 - 22:00:03 PDT
