Re: [AMBER] how to set hetrodimer for MD Simulation

From: David A Case <>
Date: Thu, 23 Nov 2017 08:21:54 -0500

On Thu, Nov 23, 2017, Rana Rehan Khalid wrote:
> My protein system consist of two subunit chains alpha and beta each chain
> consist four domains. I predicted the structure of both subunit chains now
> i want to combine both structure subunits models, How i can combine them
> in one pdb file. so that i can run the simulation on complete structure.

You should use a text editor to combine the two chains into one file. Be sure
to put a TER card at the end of each protein chain.

> I joined the structure by using pymol and try to ran the simulation but
> during minimization my simulation stop with this error
> /var/spool/torque/mom_priv/jobs/
> line 6: 2535 Segmentation fault /nfs/amino-library/local/Amber$

There is not nearly enough information here for anyone to be of any help.
We don't know what pymol did, and "Segmentation fault" just means there was an
error, but gives no information about what the error is.


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Received on Thu Nov 23 2017 - 05:30:02 PST
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