Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Wed, 17 Dec 2014 09:53:58 -0800

Adhi,

The attached output file is very useful for spotting the problem ...

It appears that you are using the sander version for the job, and the
top file is from charmm. However, no atomic charges were read in. Are
you sure your topology files and inpcrd files are correctly generated?
Please take a look in VMD first.

If you find no problem in visualizing the files. Please email me a set
of files to take a look.

Of course, I suppose you have no problem passing all the tests after
patching all the updates and installing.

All the best,
Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Dec 16, 2014 at 8:44 PM, Jason Swails <jason.swails.gmail.com> wrote:
> This error message is new to me and I don't understand why you got it.  One
> of the PBSA developers will have to chime in here.
>
> On Tue, Dec 16, 2014 at 10:56 PM, Abhishek TYAGI <atyagiaa.connect.ust.hk>
> wrote:
>>
>> Hello experts,
>>
>> I am still waiting for the reply for my problem, if some one have any clue
>> please tell me, I am stuck to this error. I am new to AMBER I am
>> understanding how to solve the error.
>>
>> Thanks in advance
>>
>> Abhi
>>
>> ________________________________________
>> From: Abhishek TYAGI
>> Sent: Monday, December 15, 2014 7:03 PM
>> To: amber.ambermd.org
>> Subject: Re: MMPBSA-ERROR for firstmolecule-dna
>>
>> Hi,
>>
>> I had added strip_mask, that helped me to solve GB calculations, but when
>> PB calculations started the new error pops out.
>>
>> The GB calculations are successful, but their is error in PB calculations
>> and I am stuck to the error "PB Bomb: pb_fdfrc: unknown ipb" in my receptor
>> output file _MMPBSA_receptor_pb.mdout.0  (attached).
>>
>> Please suggest me what to do to solve this problem. For your information,
>> I had tried the following suggestions:
>> http://archive.ambermd.org/201303/0550.html
>> http://archive.ambermd.org/201303/0550.html
>> http://archive.ambermd.org/201212/0028.html
>> http://archive.ambermd.org/201110/0485.html
>>
>> my input file is as follows:
>>
>> Input file for running PB and GB
>> &general
>>    endframe=5000, verbose=1, keep_files=2,  strip_mask=":WAT:SOD:CLA",
>> #   entropy=1,
>> /
>> &gb
>>   igb=2, saltcon=0.100
>> /
>> &pb
>>   istrng=0.100
>> /
>>
>> Please suggest me some way to solve this error
>>
>> thanks in advance
>>
>> regards
>>
>> Abhi
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Dec 17 2014 - 10:00:03 PST