Re: [AMBER] Electrostatic potential calculation

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Sat, 28 Apr 2012 21:05:32 -0700

Have you got a chance to try the latest Amber12 or AmberTool release?
It now supports both VMD and PyMol for potential visualization.

Anyway, I'm also forwarding your email to Qin to take a look ...

Ray

On Sat, Apr 28, 2012 at 5:13 AM, Sudarshan Debnath
<sudarshandebnath.ku.rediffmail.com> wrote:
> Dear All,
> † † † †I am a user of Amber11. I am trying to generate electrostatic potential surface. Follow the Amber tools11 section 7.3.2. The question is that is it mandatory to neutralize and solvate the system before create prmtop and inpcrd file for electrostatic potential surface calculation in PBSA? When I do this with solvated structure then pbsa.phi is not generated.
> I just take a portion of a pdb file (1VJ5.pdb) and create the corresponding prmtop and inpcrd file (no neutralization or salvation). Use the following parameter in input (mdin) file-
>
> PBSA visualization input
> &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 I use the following command
>
> pbsa -O -i mdin -o mdout -p prmtop -c inpcrd
>
> output file and pbsa.phi file is generated. Then I use PyMol (PyMol 1.1eval) windows version and follow the Amber tools11 section 7.3.2. The molecule is loaded by prmtop and inpcrd file. When I write the command-
>
>>load 1VJ5pbsa.phi
>
> PyMol stop working and error message is obtained, this is given below-
>
> Runtime Error!
> Program:C:\Program Files(x86)\Delano Scientific\PyMol\PyMol.exe
> This application has requested the Runtime to terminate it is an unsual way.
>
> There may be a problem with the 1VJ5pbsa.phi or PyMol. But I canít understand properly. Please let me know about this problem. I attached prmtop, inpcrd and pbsa.phi file with this mail, please check it.
>
> With best regards,
> Sudarshan
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>

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Received on Sat Apr 28 2012 - 21:30:02 PDT
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