Re: [AMBER] Electrostatic potential calculation

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 16 Apr 2012 07:12:50 -0700

Can you follow the Amber12 manual for your potential calculation? It's
discussed in section 8.4. Amber11 does not support potential
visualization by VMD.

All the best,
Ray

On Mon, Apr 16, 2012 at 6:47 AM, Sudarshan Debnath
<sudarshandebnath.ku.rediffmail.com> wrote:
> Dear Sir,
>
> Thanks for information. I am a user of Amber11. But I follow the Amber tools12 manual as you suggested. My query is simple- I want to calculate electrostatic potential by pbsa and see the surface in VMD. For a trial I take a small protein molecule made by six amino acids. Using tleap create prmtop and inpcrd for this pdb. Then follow Amber tools11 manual using the following the following input
>
>
>
> Sample PB visualization input
>
> &cntrl
>
> ntx=1,
>
> imin=1,
>
> ipb=1,
>
> inp=0
>
> /
>
> &pb
>
> npbverb=1, istrng=0, epsout=80.0, epsin=1.0,
>
> space=1., accept=0.001,
>
> sprob=1.4, cutnb=9,
>
> phiout=1, phiform=2
>
> /
>
> Then use the command
>
>
>
> ./pbsa O i **.in o **.out p **.prmtop c **.inpcrd
>
>
>
> The following script is appeared in the terminal box-
>
>
>
> Cannot match namelist object name espout
>
> namelist read: missplaced = sign
>
> cannot match namelist object name 0,
>
> cannot match namelist object name espin
>
> namelist read: missplaced = sign
>
>
>
> Then **.out file is created. But pbsa.phi.dx is not appeared. Then I follow Amber tools12 manual and use the following input-
>
>
>
> Sample PB visualization input
>
> &cntrl
>
> inp=0
>
> /
>
> &pb
>
> npbverb=1, space=1., sasopt=2,
>
> phiout=1, phiform=2
>
> /
>
>
>
> The following script is appeared in the terminal box after the same commanded is used-
>
>
>
> Cannot match namelist object name sasopt
>
> namelist read: missplaced = sign
>
>
>
> Here also **.out file is created, but pbsa.phi.dx is not appeared. I attached the input, output, prmtop and inpcrd file in this mail. What is mistake that I follow again and again? Please let me know.
>
>
>
> With best regards,
>
> Sudarshan.
>
>
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>

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Received on Mon Apr 16 2012 - 07:30:03 PDT
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