From: <wmsmith.uci.edu>
Date: Tue, Mar 19, 2013 at 3:07 PM
Subject: Re: Fwd: [AMBER] problem in generating pbsa.phi file using PBSA
To: Wesley Smith <wmsmith.uci.edu>, N Nandi <nnlabku.yahoo.com>, Ray
Luo <ray.luo.uci.edu>
Nandi,
Since I do not have your prmtop or inpcrd files, I just used what was
given in the first of the amber tutorials.
Everything seems to work ok under the most recent version of AMBER
(amber12). It runs quickly, without error, and produces the pbsa.phi file.
Do you have access to a copy of amber12?
I will dig up an old copy of amber11 and try again on the older version.
Also, can you send me a copy of the .rst and .top files?
-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
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>
>
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Received on Tue Mar 19 2013 - 15:30:02 PDT
