Did you get my last email with my suggestions? Please try those
suggestions.
On Thu, Aug 1, 2013 at 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 01 2013 - 06:30:05 PDT
