I don't think your problem is related to compilation. Failure to
recognize FE is likely because FE is not in your force field though I am
assuming that you are seeing this error in tleap/xleap, when you load the
structure/try to make prmtop/coord files.
Pete
On 8/1/13 8:57 AM, "372133720" <372133720.qq.com> wrote:
> Dear amber,
>
>I re-instal amber and the FE atom is also not recognized. 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?
>
>
>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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Received on Thu Aug 01 2013 - 06:30:06 PDT
