372133720
From: tianchuan1015
Date: 2013-07-31 15:39
To: prajwal.pharm07
Subject: Re: Re: MMPBSA problem
Dear amber,
I re-instal amber and the FE atom is also not recognized. (bad atome FE) I used intel compiler, and the _mdread.f _mdread.LES.f files are generated (which seems to me that the new mdread.f is acting) .
I wonder if the new mdread.f should be specified in the shell script?
(In the attachment, the _mdread.f and _mdread.LES.f are files generated after making serial.
The amber_MMPBSA.sh is shell script, the MMPBSA_decomp.in is input file.
The md1.log is the log file generated which writes the information of error.
The mdread.f is the new one modified by you.)
best regards
tianchuan
tianchuan1015
From: Prajwal Nandekar
Date: 2013-07-30 19:31
To: tianchuan1015
Subject: Re: Re: MMPBSA problem
I think you should look to which are the 15 errors in amber test.
The installation procedure is fine. I should run nicely.
I faced this problem many time when I initially tried to solve FE problem. I did installations many time to solve it. And finally I successfully solved it. The lesson I come to know is, Although I know the procedure of installation, but I was making simple/easy mistake during installation. And due to these mistakes I had done it many times. This is my observations.
Even when I told same procedure to my colleges, They are also make some minute mistake and they got stuck with same problem.
So I recommend you to look carefully in installation, because I cant monitor you at every step.
Because procedure is fine and it should work simply.
Regarding MMPBSA.py.MPI
My observation is, It doesn't make big difference in time of calculations using MMPBSA.py.MPI script. Instead you can simply use MMPBSA.py
Yes, For me also sometime MMPBSA.py.MPI script make me trouble. so I don't use it for energy calculation.
All the Best
On Tue, Jul 30, 2013 at 12:49 PM, tianchuan1015 <tianchuan1015.gmail.com> wrote:
Dear Prajwal Nandekar:
The installation step is in the attachment.
Besides, MMPBSA.py.MPI doesn't work, how to modify the script.(the script is also in the attachment).
Thanks for your time!
tianchuan
tianchuan1015
From: Prajwal Nandekar
Date: 2013-07-30 18:23
To: tianchuan1015
Subject: Re: Re: MMPBSA problem
Yes,
dont worry
I think you missed some step during installation.
It seems the changes made in mdread.f file is not acting.
I think you should ah=gain install Amber;
Can you please follow the steps given by me once again.
Also you write the steps followed by you in exact manner and send me back.
Then i will tell you exactly.
All the Best
On Tue, Jul 30, 2013 at 6:04 AM, tianchuan1015 <tianchuan1015.gmail.com> wrote:
Dear Prajwal Nandekar.
I have followed you procedure of re-installing amber and add the modified mdread.f. But the errors are also as follows
Beginning GB calculations with sander...
calculating complex contribution...
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
bad atom type: FE
bad atom type: FE
bad atom type: FE
bad atom type: FE
Error: sander error during GB calculations!Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Exit code -5 signaled from bnode12
Killing remote processes...MPI process terminated unexpectedly
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Is there a solution to solve this?
best regards
tianchuan1015
From: Prajwal Nandekar
Date: 2013-04-11 22:35
To: tianchuan1015
Subject: Re: Re: MMPBSA problem
Dear tianchuan,
What you have to do is that, you have to reinstall complete Amber software.
Please follow the following steps;
1) Follow all steps in Amber installation guide.
2) Extract AmberTools and install it. (Exactly as described in Amber User manual)
3) Set up the AMBERHOME environment variable to point to where the Amber tree resides
on your machine. For example
Using csh, tcsh, etc.: setenv AMBERHOME /usr/local/amber11
Using bash, sh, zsh, etc.: set AMBERHOME=/usr/local/amber11
export AMBERHOME
NOTE: Be sure to replace the "/usr/local" part above with whatever path is appropriate
for your machine. You should then add $AMBERHOME/bin to your PATH.
4) Go to the Amber web site,
http://ambermd.org, and download any bug fixes for version
11 that may have been posted. There will be a file called "bugfix.all", which is used as follows:
cd $AMBERHOME
patch -p0 -N < bugfix.all
5) After applying patch go to $AMBERHOME/src/sander/mdread.f
6) Replace old "mdread.f" file with new "mdread.f" file (download attachment of new "mdread.f" file)
(****NOTE: There are 2 places where you are required to add the values, i am
attaching the "mdread.f file" in the attachment and you go through the file
and identify the places where the changes have been named for the Fe and
then again re-install Amber.)
7) New "mdread.f" file has necessary changes made by me. And it is working fine.
8) Now compile everything:
make serial or make parallel
9) To test the basic AMBER distribution, do this:
cd $AMBERHOME/test
make test
10) Finally finish the installation and complete the test done.
Enjoy,
On Thu, Apr 11, 2013 at 7:12 PM, tianchuan1015 <tianchuan1015.gmail.com> wrote:
Thank you so much!! Take your time!
best wishes
tianchuan
tianchuan1015
From: Prajwal Nandekar
Date: 2013-04-11 22:05
To: tianchuan1015
Subject: Re: MMPBSA problem
Yes, As expected this problem is there. But don't worry, it's installation problem. I will send you detail procedure to solve this problem. Now I am quite busy but within 2 hours I will send you detail.
On Apr 11, 2013 7:00 PM, "tianchuan1015" <tianchuan1015.gmail.com> wrote:
Dear Prajwal Nandekar,
Thank you for suggestion. I reloaded and saved prmtop files.
But errors occur when I decompose the energy:
"Beginning GB calculations with sander...
calculating complex contribution...
bad atom type: FE
Error: sander error during GB calculations!"
I don't know why Fe is not identified.
tianchuan
tianchuan1015
From: Prajwal Nandekar
Date: 2013-04-11 18:31
To: tianchuan1015
Subject: Re: Re: heat process problem
Dear tianchuan1015,
Please carefully load and save the prmtop file in tlaep or xleap.
Query#1: Does this mean that even for the same system, tleap may generate different prmtop files in different times?
Answer: No. The tleap always generates same file every time.
Query#2: Error: Residue mismatch in your prmtop files! Complex res != Receptor res + Ligand res.
Answer: This is the error when the number of atoms or residues in Complex is not equal to summation of number of atoms or residues in protein and ligand prmtop files.
Suggetion: Have a look in complex, protein and ligands (see number of atoms and residues)
Please carefully load and save the prmtop file in tlaep or xleap.
On Thu, Apr 11, 2013 at 1:56 PM, tianchuan1015 <tianchuan1015.gmail.com> wrote:
Dear Prajwal Nandekar,
I want to use mmpbsa to do analysis. But I didn't save protein.prmtop and complex.prmtop when I prepare my system in tleap before. Thus I load them in tleap again and save prmtop files. However ,error goes like as follows:
Error: Residue mismatch in your prmtop files! Complex res != Receptor res + Ligand res.
Does this mean that even for the same system, tleap may generate different prmtop files in different times? Is there a way to solve this problem?
best regards
tianchuan
--
Thanks and Regards,
---------------------------------------------
Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mob. 09780741228
--
Thanks and Regards,
---------------------------------------------
Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mob. 09780741228
--
Thanks and Regards,
---------------------------------------------
Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mobile: +49-15163953926
--
Thanks and Regards,
---------------------------------------------
Prajwal Nandekar
Ph. D. Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mobile: +49-15163953926
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- application/octet-stream attachment: _mdread.f
- application/octet-stream attachment: mdread.f
- application/octet-stream attachment: md1.log
Received on Wed Jul 31 2013 - 19:30:03 PDT
