From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Oct 18 2010 - 11:40:28 CDT
You are trying to write the dcd file in "/", the root directory, which is
typically not writable by anyone except root.
-Jim
On Mon, 18 Oct 2010, Christian Jorgensen wrote:
> Hi,
> I am trying to do a second run on a simulation of a solvated dipeptide. I have successfully run 2 simulations on both of two of the three protonated states of the peptide, but for the third protonation state during the second (restart) run I encounter the following problem:
>
> Reason: FATAL ERROR: Couldn't open DCD file /run2_solvatedpeptide.dcd: Permission denied
>
> Charm++ fatal error:
> FATAL ERROR: Couldn't open DCD file /run2_solvatedpeptide.dcd: Permission denied
>
>
> I have checked to see that the respective files generated in the first run are where they have to be.
>
> Any help would be appreciated
>
> Christian Jorgensen
> PTCL
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of sunita gupta [sunita.bio_at_gmail.com]
> Sent: Monday, October 18, 2010 12:52 PM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: High RMSD of Coarse grain Protein
>
> Hello all
>
> I did coarse grain simulation of protein (92 residues), the RMSD of the protein is in the range of 1.5 till a small restraints is on the protein beads and as i remove all the restraints (in production).the RMSD shoots up to 6.5 Armstrong . Also I am not able to get back the all-atom structure from coarse grain trajectory , as the secondary structure is completely lost.
> Can any one help me with this sudden rise in RMSD and how to reverse bank the coarse grain data to all-atom pdb?
>
> Thanks in Advance
>
>
> --
> --
> SUNITA GUPTA
>
>
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