On Mon, Aug 19, 2013 at 8:35 AM, Thomas Evangelidis <tevang3.gmail.com>wrote:
> Hi Jason,
>
> It didn't work. I loaded the reordered .prmtop and .rst files in VMD and
> saw wrong bonding between the protein atoms. When I tried to run NPT
> equilibration using these files with pmemd.cuda I got:
>
> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
>
> whilst with pmemd.mpi:
>
> | ERROR: PMEMD does not support intermolecular PRFs!
>
> I 'll send you my files to your gmail to see if you can find what's wrong.
> Just to tell you that I have followed the same protocol for another protein
> that differs only in one amino acid and worked perfectly fine.
>
I need the prmtop and inpcrd in order to debug. Or the original PDB
file...
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Aug 19 2013 - 10:30:03 PDT
