Re: Explicit Membrane Protein Simulations in NAMD/VMD

From: Richard Law (drrichjlaw_at_gmail.com)
Date: Thu Aug 28 2008 - 15:40:10 CDT

I think we determined that the problem was that not all the atoms were
present in the constraints input files.

On 8/28/08, Jerome Henin <jhenin_at_cmm.chem.upenn.edu> wrote:
> 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
>>
>>
>
>
>

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++YNWA
Dr. Richard J. Law
Biosciences & Biotechnology Division
Chemistry, Materials, Energy and Life Sciences Directorate
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