Re: [AMBER] MMPBSA error

From: zahra khatti <zkhatti2000.yahoo.com>
Date: Fri, 6 Jun 2014 05:57:41 -0700 (PDT)

Dear Dr. Ray

In my case all atoms of nanotube have approximately neutral charge.
This is my input file of mmpbsa:
Input file for running PB
&general
endframe=50, verbose=1,
/
&pb
/
could I run mmpbsa for free binding energy calculation?
best regards.

 
Z. Khatti, Ph.D student of Physical Chemistry,
Department of Chemistry, Iran University of Science & Technology,Tehran, Iran

On Friday, June 6, 2014 3:57 AM, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote:
 


Zahra,

One reason for the reported failure is that the receptor has not a
single atom charged … the force driver simply skip the call to
pb_force() in this situation. This is probably too crude for you since
your nanotube was built with neutral atoms on purpose. This is not a
negligence. I'll supply an update to allow van der Waals calculation
to go through in this situation ...

I'm trying to understand why the program complaints about the non
bonded list for the complex that does contains charged atoms …

All the best,
Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Wed, Jun 4, 2014 at 10:52 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Zahra,
>
> Can you email me off the list your prmtop/inpcrd to take a look? There
> shouldn't be such error messages any more after our recent updates.
>
> Did you patch all updates and pass the tests for AmberTools 13?
>
> Ray
>
> On Jun 4, 2014 6:01 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>>
>> On Tue, 2014-06-03 at 13:17 -0700, zahra khatti wrote:
>> > AmberTools13
>>
>> I'm not sure what the "correct" fix for this problem is.  You can try
>> googling the error message, which will bring up previous threads that
>> may help you solve the problem.
>>
>> You can also try increasing the maxnba estimate in
>> $AMBERHOME/AmberTools/src/pbsa/pb_init.F90 (look at line 215) if none of
>> the suggestions from past email threads work.
>>
>> You can print out the value of eclose +
 pclose + sclose + nclose + cntr
>> as well as maxnba in pb_list.F90 (~line 699) to see how much bigger you
>> need to make maxnba.
>>
>> If none of these work, I'll have to defer to a PBSA developer.
>>
>> Good luck,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
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Received on Fri Jun 06 2014 - 06:30:02 PDT