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

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 19 Dec 2014 10:25:23 -0800

THanks for the heads up …

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 10:15 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
>> On Dec 19, 2014, at 12:47 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>>
>> 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 …
>
> 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.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Fri Dec 19 2014 - 10:30:03 PST
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