Hello Ray Luo,
Thanks for your relpy. Can you tell me who is the MJ you've refered and give me his email.Besides,can you give me the right link to the Amber10 patch,you've reminded me whether I have done the right patching.
Thank you!
2010-01-27
geyan
发件人： Ray Luo
发送时间： 2010-01-27 03:01:36
收件人： AMBER Mailing List
抄送： MengJuei Hsieh
主题： Re: [AMBER] need help in MM_PBSA calculation
Most likely the patching was done wrong if you are talking about Amber10
here ... please ask MJ for some suggestion on this. I've cc'ed him on
this ...
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/
==========================================
geyan wrote:
> Dear Amber-users,
> I met another problem in calculating the MM_PBSA.At first I can get the snapshot_statistics.out file but the PBSUR and GBSUR is zero,which is apparently a mistake. Following the suggestions of somebody in this Amber maillist,I update the Amber with latest patch.But after updating,I got an unexpected error early than before.
> Before updating,I can get the three "snapshot_*.all.out file" and an incomplete all.statistics.out file ,however,after updating,I can only get the wrong snapshot_com.all.out file,which reads as follows
> MM
> GB
> PB
> MS
> PB_SURFTEN 0.0072
> PB_SURFOFF 0.00
> 1
>
> And the error file reads,
>
> Use of uninitialized value in concatenation (.) or string at /soft/x86_64/apps/OpenSoft/Chem/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 191.
> Can't exec "-O": No such file or directory at /soft/x86_64/apps/OpenSoft/Chem/amber10/src/mm_pbsa/mm_pbsa_calceneent.pm line 197.
> -O -i sander_com.in -o sander_com.1.out -c /home_soft/home/wujy/Geyan/Amber/MM_PBSA/snapshot_com.crd.1 -p /home_soft/home/wujy/Geyan/Amber/MM_PBSA/ras-raf.prmtop not successful
>
> Do anybody konw why?
> Thanks very much!
> 2010-01-26
>
>
>
> geyan
>
>
>
> 发件人： geyan
> 发送时间： 2010-01-21 19:39:16
> 收件人： Shulin Zhuang
> 抄送：
> 主题： Re: Re: [AMBER] need help in MM_PBSA calculation
>
>
> Thank you,Shulin. But I have a problem,I don't have the pemission to modefy the Amber suit,which is installed in a public server. Now that I have already got the three all.out file that is snapshot_com.all.out, snapshot_rec.all.out and snapshot_lig.all.out,I think the next step is to calculate the statistics.out file with the correct mm_pbsa_statistics.pm package. So do you have a correct copy of it and deliver me one by attach?Whether I can run it standalone?
> Thanks again for your kindly reply.
>
> 2010-01-21
>
>
>
> geyan
>
>
>
> 发件人： Shulin Zhuang
> 发送时间： 2010-01-21 17:28:45
> 收件人： geyan
> 抄送：
> 主题： Re: [AMBER] need help in MM_PBSA calculation
> . One more word. Your problem is because of the bug in amber10. Just download the amber10 bugfix.all:http://ambermd.org/bugfixes10.html
>
>
> On Thu, Jan 21, 2010 at 1:27 AM, Shulin Zhuang <shulin.zhuang.gmail.com> wrote:
>
> Hi, Geyan, you need to fix the bug in mm_pbsa.pm. Good luck!
>
>
> 2010/1/21 geyan <geyan.big.ac.cn>
>
>
> Dear Amber_users,
> I have met a problem in performing the MM_PBSA analysis. Following the MM_PBSA section of Amber tutorial,I can't accomplish the bind_energy calulation
> with the error says,"No data for 0+0 PB ELRAELE 0". Besides,the output file also gives the error message like,"
> WARNING: Missing PBNONPOL for PB in 160 -> Taken from 159
> WARNING: Missing ELRAELE for PB in 160 -> Taken from 159
> WARNING: Missing EPB for PB in 160 -> Taken from 159"
> I searched this problem in Google,finding the solution by changing index 0 of ELRAELE, EPB, PBNONPOL in mm_pbsa_statistics.pm to 0 and
> "Use the snapshot_statistics dot in as the input file, assign an output file
> and if you have the snapshots of com, rec and lig from three different
> trajectories, set calc_delta = 2. If you had extracted the snapshots from
> the same trajectory, set calc_delta = 1. For both cases, you can set
> calc_decomp to 0. " this paragraph is what I directly copy from the internet.
> Truely,it does work in some degree. But after comparing with the exact result download from the tutorial,my result have a clear mistake,that is the item PBSUR and GBSUR is zero in every respect as follows,and other figures is slightly different with the standed result.
> So,just changing the above parameters is not sufficient to solve the problem,can anybody help me? I am very eager to receive your replies.
> Thank you very much!
> GeYan
> # COMPLEX RECEPTOR LIGAND
> # ----------------------- ----------------------- -----------------------
> # MEAN STD MEAN STD MEAN STD
> # ======================= ======================= =======================
> ELE -8656.78 70.18 -5602.09 63.10 -2102.25 52.57
> VDW -984.99 24.34 -661.18 20.33 -256.02 12.93
> INT 5085.33 50.22 3449.57 38.65 1635.76 29.42
> GAS -4556.44 75.96 -2813.70 65.21 -722.52 53.50
> PBSUR 0.00 0.00 0.00 0.00 0.00 0.00
> PBCAL -3244.39 59.67 -2516.48 50.04 -1672.39 47.87
> PBSOL -3244.39 59.67 -2516.48 50.04 -1672.39 47.87
> PBELE -11901.17 33.10 -8118.58 28.08 -3774.64 16.64
> PBTOT -7800.82 48.10 -5330.18 36.70 -2394.91 26.71
> GBSUR 0.00 0.00 0.00 0.00 0.00 0.00
> GB -3250.03 59.24 -2540.49 50.86 -1672.13 48.22
> GBSOL -3250.03 59.24 -2540.49 50.86 -1672.13 48.22
> GBELE -11906.80 27.15 -8142.59 23.52 -3774.38 13.43
> GBTOT -7806.46 47.32 -5354.19 35.95 -2394.64 27.08
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -952.43 44.10
> VDW -67.79 5.18
> INT -0.00 0.00
> GAS -1020.22 44.58
> PBSUR 0.00 0.00
> PBCAL 944.49 43.14
> PBSOL 944.49 43.14
> PBELE -7.95 9.81
> PBTOT -75.73 8.32
> GBSUR 0.00 0.00
> GB 962.59 41.40
> GBSOL 962.59 41.40
> GBELE 10.16 7.77
> GBTOT -57.63 6.52
>
>
>
> 2010-01-21
>
>
>
> geyan
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>
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>
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Received on Tue Jan 26 2010 - 19:00:02 PST
