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

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 19 Dec 2014 09:47:39 -0800

Abhi,

Just to reply on the list for the sake of tracking …

Something wrong with the prmtop files that were generated … I couldn't
load any one (ligand/receptor/complex/solvated complex) into VMD …

How did you get these files converted from? Some other developers may
chime in on this …

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 Fri, Dec 19, 2014 at 1:14 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk> wrote:
> Dear Prof Luo,
>
>
> Thank you for your reply.
>
>
> Prof Luo for your information I am sending you my inpcrd and prmtop files, please have a look for the errors, i am sending these files to the
>
> email: ray.luo.uci.edu.
>
>
> If I need to send anything else that I missed please let me know.
>
>
> I checked installation on my PC, I had recently reinstalled AMBERTOOL14 and AMBER14, and tried tutorials, they are working fine and I had successfully finished the tutorials on this version, than I had converted my original psf, pdb, topology,parameter files using CHAMBER to prmtop and inpcrd and i am using dcd file obtained from NAMD file format to perform MMPBSA calculations.
>
>
> with best regards
>
>
> Abhi
>
>
>
> Date: Wed, 17 Dec 2014 09:53:58 -0800
> From: "Ray Luo, Ph.D." <ray.luo.uci.edu>
> Subject: Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <CALRp-wpet6SZskdikck37rVv616n09vQ90ti_37s+5RXoygHUA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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
>>>
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Received on Fri Dec 19 2014 - 10:00:02 PST