AMBER Archive (2004)

Subject: Re: Re: Re: AMBER: Why the surface calculations sometimes fail?

From: David A. Case (
Date: Thu Dec 16 2004 - 11:32:29 CST

On Thu, Dec 16, 2004, hj zou wrote:
> Sorry for the delay. Please find enclosed as attachment the requested
> parmtop file.

I am not able to reproduce your problem. I had to guess some: you sent all
kinds of file, but never the actual "pqr" file that is input to molsurf. But
I converted your "9.pdb" file myself, and used molsurf to calculate both the
molecular surface and and solvent accessible surface; neither gave a problem.

So I guess we will need more information: what version of Amber, which OS and
compiler, exactly what is the output from molsurf.


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