RE: Explicit Membrane Protein Simulations in NAMD/VMD

From: Shultz, Jack (JShultz_at_nas.edu)
Date: Thu Aug 28 2008 - 15:07:24 CDT

I exchanged emails with Richard and he thinks I need to modify these
lines and generate a conskfile. I'll try it later.

> In your restrained_md_example.in you have:
>
> consref protein_only.coor
> conskfile protein_cons.pdb

-----Original Message-----
From: heninj_at_gmail.com [mailto:heninj_at_gmail.com] On Behalf Of Jerome
Henin
Sent: Thursday, August 28, 2008 3:57 PM
To: Shultz, Jack
Cc: NAMD list
Subject: Re: namd-l: Explicit Membrane Protein Simulations in NAMD/VMD

Is restr_min_nachr.coor a binary file?

Jerome

On Thu, Aug 28, 2008 at 1:25 PM, Shultz, Jack <JShultz_at_nas.edu> wrote:
>
> Has anyone tried this membrane tutorial?
> http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm
>
> I am running other NAMD tutorials fine, but after I run the first
> minimization simulation (step 7) which runs successfully, I run step 8
> Equilibration and I get this error. And I did check to see the number
of
> atoms (14737) is consistent with the number in the psf, pdb and vel
> files. Does anyone have any advice?
>
> Info: 0 VDW_PAIRS
> FATAL ERROR: Incorrect atom count in binary file restr_min_nachr.coor
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Incorrect atom count in binary file
> restr_min_nachr.coor
>
> Charm++ fatal error:
> FATAL ERROR: Incorrect atom count in binary file restr_min_nachr.coor
>
>
> abnormal program termination
>
>

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