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.
best,
Thomas
On 19 August 2013 04:03, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, Aug 18, 2013 at 7:17 PM, Thomas Evangelidis <tevang3.gmail.com
> >wrote:
>
> > Dear AMBER list,
> >
> > How do I get this error at unrestrained NPT equilibration since I can
> load
> > and visualize in VMD the prmtop and .rst file from NVT equilibration?
> > The number of atoms in the .rst file is the same as in the .prmtop. Below
> > is the configuration file I used in NVT.
> >
>
> This is a bug in tleap that results when you combine two separate molecules
> using the 'bond' command in tleap. It is a bug in tleap that is known, but
> has not yet been fixed.
>
> There is a relatively simple workaround in either cpptraj or ParmEd (make
> sure you have AmberTools 13 fully up-to-date).
>
> Using ParmEd, try this:
>
> parmed.py -p <your_prmtop> << EOF
> loadRestrt <your_restart>
> setMolecules solute_ions True
> parmout <reordered_prmtop> <reordered_restrt>
> EOF
>
> reordered_prmtop and reordered_restrt should then work.
>
> The error, in case you are curious, is that the SOLVENT_POINTERS and
> ATOMS_PER_MOLECULE sections of the prmtop are structured under the
> assumption that all of the molecules are composed of consecutive atoms.
> However, if molecules 1 and 3 are combined via a 'bond' command in tleap,
> then the atoms are not properly reordered to satisfy this assumption. This
> results in a broken ATOMS_PER_MOLECULE section of the prmtop which can
> later result in very strange errors (e.g., segfaults) in sander and pmemd.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Mon Aug 19 2013 - 06:00:04 PDT
