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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Received on Tue Jan 26 2010 - 01:00:04 PST
