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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 26 2010 - 11:30:03 PST
