AMBER Archive (2009)

Subject: Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR

From: Ashish Runthala (
Date: Thu Jul 30 2009 - 22:40:45 CDT

you used solvatecap which has made an array but the velocities are
assigned zero in all three directions of the velocity vector(0,0,0)
And hence the sander being smart enough halts the script saying a
segmentation fault.
Just check your pdb file again, making its confirmation detail proper
to be used for the sander.

On Fri, Jul 31, 2009 at 7:28 AM, Brothers, Michael
Charles<> wrote:
> Dear Amber Users,
> I attached my original PDB file (33GMBS.pdb), my modified .oFF file from RED with protecting groups, my modified .oFF file from RED without protecting groups, and the PDB file that resulted (A.pdb).
> I have the following errors:
> 1) If I use my .oFF file with the protecting groups, it reinserts them automatically (
> 2) If I use my .oFF file with the protecting groups removed (manually), it claims that there is a segmentation fault and shuts down the program (
> Any ideas/suggestions?
> Thanks,
> Mike
> _______________________________________________
> AMBER mailing list

Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031

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