Nandi,
From what I can see, it looks like you are getting a segmentation
fault, meaning the program is experiencing an internal memory error
somewhere. I will see if I can replicate the error so I can figure out
what the problem is. I will send another email once I have an idea of
what is going on.
If you can forward the prmtop and inpcrd files that may help speed things up.
-Wes
> I'm forwarding to Wes, who's an expert in visualizing ...
>
> Ray
>
> ---------- Forwarded message ----------
> From: N Nandi <nnlabku.yahoo.com>
> Date: Sun, Mar 17, 2013 at 10:15 PM
> Subject: [AMBER] problem in generating pbsa.phi file using PBSA
> To: "amber.ambermd.org" <amber.ambermd.org>
>
>
> Dear All,
> We plan to visualize the electrostatic potential map of a pdb (DNA
> double helix) through PyMol. For this we need to generate the pbsa.phi
> file using PBSA. We are user of AMBER11 (version 1.4). For this
> purpose we used the pdb nuc.pdb and also generate the prmtop and
> inpcrd file. The problems are:
> 1.no pbsa.phi file was generated
> 2.we get the following script on the terminal:
> segmentation fault
> The input used is given below:
> pbsa test
> &cntrl
> ntx=1,
> imin=1,
> maxcyc=10000,
> ipb=1,
> inp=0,
> /
> &pb
> npbverb=1,
> istrng=0,
> epsout=80.0,
> epsin=1.0,
> space=1.0,
> accept=0.001,
> sprob=1.4,
> cutnb=2,
> phiout=1,
> phiform=0
> /
> then we used the following command:
> ./pbsa -O -i mdin -o mdout -p nuc.top -c nuc.rst
> We shall be thankful to know how the pbsa.phi file can be generated.
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Mar 18 2013 - 15:00:02 PDT
