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

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 19 Dec 2014 15:48:03 -0800

Abhi,

Okay, it turns out that sander is trying to proceed with the PB
calculation even if ipb is set to zero because the good old flag igb =
10 is also used in the sander force() driver.

The ipb flag has been set to zero, i.e. bypassing PB, when the
initialization routine cannot detect a single charge in the system.
I'll submit a patch to reset igb value as well so PB won't be
triggered.

Thanks a lot for reporting! While I'm working on the patch, you can
safely set all electrostatic energies and PB/GB energies to zero for
the identically neutral receptor.

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 11:00 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Fri, Dec 19, 2014 at 11:15 AM, Jason Swails <jason.swails.gmail.com> wrote:
>> These are chamber-generated prmtop files.  They are not compatible with VMD.  You should be able to load them into cpptraj, though.  You can use cpptraj to generate a PDB file you can visualize in VMD if you need to.
>
> FYI you can also "strip" the chamber info from the topology for use
> with VMD with cpptraj 'parmwrite' command with the 'nochamber'
> keyword, but the topology is then good for visualization/analysis
> only, *not* simulations.
>
> parm myparm.parm7
> parmwrite out nochamber.parm7 nochamber
>
> -Dan
>
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Fri Dec 19 2014 - 16:00:03 PST