Re: Re: [AMBER] error when doing MMPBSA

From: pxq <pangxueqintea.yahoo.com.cn>
Date: Mon, 22 Mar 2010 16:51:44 +0800

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 - 02:00:03 PDT
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